This DM would rule that a creature cannot have a spell modified by a metamagic effect as a spell-like ability
There aren't many opportunities for a creature to pick its own spell-like ability. For example, the prestige class archmage (DMG 178-9) grants the creature that takes the class the option of picking a spell-like ability, and the feats Innate Magic (Dragon #324 78) and Innate Spell (CAr 80) allow a creature to pick a spell to have as a spell-like ability. However, in all the other cases I'm familiar with except the archmage's, the text is silent as to whether a creature can pick as a spell-like ability a spell modified by a metamagic effect, and this DM is uncomfortable—on several levels—with viewing silence as permission.
To find some kind of further confirmation, I searched all five Monster Manuals and the Fiend Folio, and while each text has creatures that employ, for example, quickened spell-like abilities, none of the creatures in any of those texts have spell-like abilities that are quickened without having used the feat Quicken Spell-like Ability (e.g.
the deathdrinker (MM4 40-1), the jahi (MM2 130-1), the mindshredder zenthal (MM3 104-5), the octopus tree (FF 130-2), the remmanon (MM5 34-5), the titan (MM 242-3)). As a monster designer could have just given the creature the spell-like ability as quickened spell instead of having the creature take the feat Quicken Spell-like Ability, it appears that monster designers just don't do that, and that's enough for this DM to say no. (I am certain that outside these texts there're monsters that have spell-like abilities that're naturally modified by a metamagic effect, but I figure most folks will look for example monsters in Monster Manuals to guide their decisions rather than using edgier cases as examples.)
So, as usually PCs aren't given greater leeway than monsters in the special abilities they can have (really, it's usually the other way around), this DM would not allow a PC that gets to pick a spell-like ability to pick a spell modified by a metamagic effect as a spell-like ability. Instead, the PC should take a feat that affects the spell-like like ability with the metamagic effect the PC wants, and a feat that modifies a spell-like ability with a metamagic effect like the one he wants doesn't exist (for example, the player is lamenting that the metamagic feat Energy Substitution (Shadowdale: The Scouring of the Land 149) has no corresponding feat Energy Substituted Spell-like Ability), the DM should probably simply create such a feat rather than allow the spell that's picked as a spell-like ability to be modified by a metamagic effect.
In particular, on the template spellstitched
The template spellstitched (Complete Arcane 161-2) says
Spellstitched creatures can be created only by a wizard or sorcerer with the Craft Wondrous Item feat and of sufficient level to cast the spells to be imbued within the undead’s body. The creation process takes a number of days equal to the Wisdom score of the undead creature being spellstitched (so a minimum of 10 days) and requires the expenditure of 1,000 gp for carving or tattooing materials in addition to 500 XP × the undead creature’s Wisdom score. Undead with arcane spellcasting abilities can spellstitch themselves. (161)
Emphases mine. This means the wizard or sorcerer (not a bard, beguiler, duskblade, hexblade, or spellthief, mind you—only a socerer or wizard) applying the spellstitched template to itself or another can pick any conjuration, evocation, or necromancy spell that's of a spell level it can cast, but that picked spell need not be a spell the sorcerer or wizard can cast, nor does that spell need to even be on the sorcerer or wizard's spell list! So for 5,500 XP (or 27,500 gp if an undead creature can find a sorcerer or wizard to spellstitch it on the creature's behalf)1 an undead creature with a Wisdom score of 19 at the time the template spell-stitched is applied and that has a caster level of at least 11 (or has a sorcerer or wizard buddy that does) can have a wildly diverse and—with some Dumpster-diving—extremely powerful suite of spell-like abilities that are otherwise difficult to acquire (e.g. the 8th-level Clr spell summon giants [conj] (Frostburn 105) is a 4th-level spell for the prestige class disciple of Thrym (Fr 56-8)). For example, even just using the core rules, a spellstitched creature's spell-like abilities could look like this:
Spell-like Abilities: 2/day—command undead, desecrate, grease, shield; 1/day—animate dead, create undead (or greater shout), divine power, lesser planar ally, lesser planar binding, raise dead, wind wall.
That's a power suite I think few would argue is weakened significantly by the lack of metamagic effects applied to the spells.
This DM would argue that this absurd diversity more than makes up for the spellstitched creature's inability to pick as a spell-like ability, for example, quickened magic missile. Also, considering that a creature that's already been the subject of the template spellstitched once remains, technically, still a valid target for the template spellstitched, there exists the controversial possibility of acquiring the template spell-stitched multiple times, but good luck finding any DM that will allow that. (This DM would rule the templates' named special abilities—including the one named spell-like abilities—overlap instead of combine, but another DM may rule differently.)
"Wait a second… LA +1?"
A comment by the question's author mentioned that spellstitched "is being treated as a LA +1 template during character creation in a low level but high-power campaign." Possessing spell resistance alone is usually enough for Wizards of the Coast to bump a creature's Level Adjustment by +1. And, while this DM sees that as an overreaction (SR can be as much burden as gift at low levels), the template spellstitched also grants DR, turn resistance, and an otherwise-difficult-to-get +2 profane bonus on saving throws in addition to spell-like abilities of, potentially, ridiculous power. Unless playing in a really, really high-powered game, consider increasing the template's level adjustment to at least +2 or even higher depending on how high the creature's Wisdom was pumped during the template's acquisition and how deep into the Dumpster the creator's dived to pick the creature's spell-like abilities.
1 Assuming a Wisdom 19 undead creature's acquiring the template spellstitched. And if the creature possesses less than Wisdom 19 add to the price maybe 4 castings per day for 19 days of the 5th-level Drd spell an owl's insight [trans] (Spell Compendium 152) modified by the feat Extend Spell costing 660 gp for each owl's insight spell therefore 2,640 gp per day therefore 50,160 gp for 19 days. Seriously, if you're gonna do it, do it right.