There are two ways you could get around this, and neither includes Scribe Scroll.
Note: This method is exclusive to Pathfinder, as D&D 3.5 Mystic Theurge does not have "Combined Spells".
I refer you to here:
Combined Spells (Su):
A mystic theurge can prepare and cast spells from one of his spellcasting classes using the available slots from any of his other spellcasting classes. Spells prepared or cast in this way take up a slot one level higher than they originally occupied. This ability cannot be used to cast a spell at a lower level if that spell exists on both spell lists. At 1st level, a mystic theurge can prepare 1st-level spells from one of his spellcasting classes using the 2nd-level slots of the other spellcasting class. Every two levels thereafter, the level of spells that can be cast in this way increases by one, to a maximum of 5th-level spells at 9th level (these spells would take up 6th-level spell slots).
So, a Favored Soul/Wizard/Mystic Theurge, can prepare Divine Spells of up to 5th level as 6th level Arcane Spells. We can agree on that. Cool.
The components of these spells do not change, but they otherwise follow the rules for the spellcasting class used to cast the spell.
Let's take Comprehend Languages as it appears on both lists as a 1st level spell.
To cast it:
A Wizard requires an Arcane Material (A pinch of soot and few grains of salt).
A Favored Soul need only hold their Holy Symbol during the ritual.
So, if your Mystic Theurge knows Comprehend Languages as a Favored Soul, she would:
1. Prepare Comprehend Languages using a 2nd level Wizard slot.
2. When ready to cast the spell, she would hold her Divine Symbol.
3. Upon casting the spell, Comprehend Languages is an Arcane spell, subject to arcane failure rates.
Effectively, the end result is an entirely new spell. Comprehend Languages powered by arcane energy using a divine focus. This is different to both iterations of the spell currently in play.
Alternative to casting the spell, once our Mystic Theurge has prepare Comprehend Languages in a 2nd level Wizard slot, she could write it down into her Wizard Spellbook following the same rules as laid out in Replacing Spellbooks, found here:
Replacing and Copying Spellbooks:
If he already has a particular spell prepared, he can write it directly into a new book at the same cost required to write a spell into a spellbook. The process wipes the prepared spell from his mind, just as casting it would.
He has Comprehend Languages prepared in his Arcane Spell slot. It is completely within the rules for him to then copy that spell into his Spellbook.
Of course, our Mystic Theurge could take the extra step of scribing it as a scroll (which would be Arcane, and unable to be used by a regular divine caster). Although such a step would be a costly, unnecessary time sync.
This method would need one assumption to be made:
What level would the newly created spell be?
I believe it will be the level it was prepared as when copied down into the spellbook.
Arcane Comprehend Languages - Level 1 Wizard
Divine Comprehend Languages - Level 1 Cleric (Favored Soul)
New Comprehend Languages - Level 2 Wizard
Still refering to Arcane Magical Writings:
A wizard can also research a spell independently, duplicating an existing spell or creating an entirely new one. The cost to research a new spell, and the time required, are left up to GM discretion, but it should probably take at least 1 week and cost at least 1,000 gp per level of the spell to be researched. This should also require a number of Spellcraft and Knowledge (arcana) checks.
Here, our Wizard/Favored Soul, even without Mystic Theurge levels (or for spells above 6th level), is able to create new versions of her spells.
Sticking with Comprehend Languages, our Wizard/Favoured Soul knows the effect "Comprehend Languages" is possible through magic using divine energy. Through her studies in the Arcane, she would be able to:
A) Find correspondences between Arcane and Divine procedures that result in similar effects.
B) Through her raw knowledge of Arcane materials, she can experiment with components until she discovers the right ones to produce Comprehend Languages as an arcane caster.
Both of these methods would result in our Wizard/Favored Soul discovering Comprehend Languages in arcane form as it appears in the SRD.
Extrapolating from this, and if allowed by a DM, a character with levels as a Wizard/Favored Soul, would be able to create Arcane versions of all Divine Spells known to the Favored Soul half. Although such antics are likely to get denied by a DM.
Now, regarding the use of scrolls in this situation and why it isn't possible, I begin by refering you to search "Divine Spells" for Pathfinder (I cannot link more). You will find in the first paragraph:
Clerics, druids, experienced paladins, and experienced rangers can cast divine spells. Unlike arcane spells, divine spells draw power from a divine source. Clerics gain spell power from deities or from divine forces. The divine force of nature powers druid and ranger spells, and the divine forces of law and good power paladin spells.
Divine spells are powered by Divine Energy. Arcane spells are powered by a different source. What source? It's anybody's guess, but it ain't Divine.
If you search Pathfinder Scrolls, you'll come to this entry:
Decipher the Writing
The writing on a scroll must be deciphered before a character can use it or know exactly what spell it contains. This requires a read magic spell or a successful Spellcraft check (DC 20 + spell level). Deciphering a scroll is a full-round action.
Deciphering a scroll to determine its contents does not activate its magic unless it is a specially prepared cursed scroll. A character can decipher the writing on a scroll in advance so that she can proceed directly to the next step when the time comes to use the scroll.
Anybody, even non-spellcasters, can determine the nature of a scroll (What spell it contains and whether it's divine/arcane) so long as they're skilled enough.
Activating the Spell
To have any chance of activating a scroll spell, the scroll user must meet the following requirements.
• The spell must be of the correct type (arcane or divine). Arcane spellcasters (wizards, sorcerers, and bards) can only use scrolls containing arcane spells, and divine spellcasters (clerics, druids, paladins, and rangers) can only use scrolls containing divine spells. (The type of scroll a character creates is also determined by his class.)
• The user must have the spell on her class list.
• The user must have the requisite ability score.
Here we are explicitly told an Arcane user can only activate an Arcane spell.
The writing for an activated spell disappears from the scroll as the spell is cast.
I'll come back to this one in just a moment.
If we go back to Arcane Magical Writings, we come to:
Spells Copied form Another's Spellbook or a Scroll
A wizard can also add a spell to his book whenever he encounters one on a magic scroll or in another wizard's spellbook. No matter what the spell's source, the wizard must first decipher the magical writing (see Arcane Magical Writings).
The quote argued above saying "No matter what the spell's source..." does not refer to the nature of divine or arcane, but where the spell is being drawn from: spellbook, scroll, etc. This renders that point moot. Regardless of how you feel about this interpretation, we end up at the same place which is: "Decipher the Magical Writing", which we touched on above.
Personally, it's at this point that the Arcane caster finds the Divine Scroll useless in terms of copying into his spellbook. Once he discovers it's Divine, he would understand it's of no use to him. But let's continue to find out why he would draw this conclusion.
The process leaves a spellbook that was copied from unharmed, but a spell successfully copied from a magic scroll disappears from the parchment.
While this doesn't explicitly state that copying from a scroll into a spellbook is an act of "activating" a spell, it does help build an argument. Both situations result in the spell disappearing from the parchment.
Such an argument is further supported by:
Replacing and Copying Spellbooks
A wizard can use the procedure for learning a spell to reconstruct a lost spellbook. If he already has a particular spell prepared, he can write it directly into a new book at the same cost required to write a spell into a spellbook. The process wipes the prepared spell from his mind, just as casting it would. If he does not have the spell prepared, he can prepare it from a borrowed spellbook and then write it into a new book.
Here, writing a prepared spell into a spellbook, works much as casting it would. While the spell hasn't technically been cast, it requires much of the same energy (An arcane spell slot).
Thus if copying from memory works like casting, copying from a scroll works like activating the scroll. If you cannot activate it, you cannot copy it.
I understand that this interpretation of the rules might not work for some people because it's not explicitly stated. That's okay.
Even ignoring such a conclusion and you allow your Wizard to copy a Divine spell into his Spellbook, his Wizard class does not provide him with any Divine spell slots. He would be unable to prepare the spell as a Wizard because it's powered by divine energy, which he has none of for that class.
If this were a scroll he found in the wild and copied into his spellbook, his divine caster would not be able to prepare from it unless it had Archivist mechanics, where by it prepares spells as a Wizard does. As we know of from above, most divine casters pray for their spells which are granted to them by their patron deities. Most would be unable to prepare from written instructions.