The end result is as you might expect: you can pump the spell’s spell level as high as you have turn or rebuke undead attempts to pay for, to a maximum of 9th level, and your own spell access has nothing to do with it.
But I think the real question is, how do we determine that this is the result?
The best answer, to my mind, is because Races of Destiny says so:
If she chooses to apply the Heighten Spell effect, [naenhoon] costs her one turn attempt per level that she heightens the spell, up to a maximum of 9th level.
(Races of Destiny pg. 55)
But even if it didn’t say that—or you don’t think that’s explicit enough—we can still determine the same result from the other rules.
So let’s go through the interaction carefully. It’s best to do that step-by-step, and the way metamagic feats are worded—and the way naenhoon is worded—the first step is to apply the metamagic. So we start by applying Heighten Spell to secret weapon, which is otherwise a 1st-level spell for a wizard.¹ Figuring out, and paying, the cost of the metamagic is actually the last step.
Heighten Spell tells us that the spell’s spell level becomes “higher than normal (up to a maximum of 9th level),” and that it “is as difficult to prepare and cast as a spell of its effective level.”
Left unsaid, technically, is how you determine which level that is, between the spell’s level and 9th, but reading between the lines, it’s fairly clear that this is the caster’s choice. This is problematic, though, because now we are asking exactly what the options are, and since they didn’t even bother to write out that the caster is the one making the choice, they certainly didn’t truly spell out what the caster’s options are. But since the feat does state a lower bound (“higher than normal”) and an upper bound (“maximum of 9th level”), one presumes if any stricter boundaries than this were intended, they’d be written.
Moreover, numerous effects explicitly refer to applying Heighten Spell without paying for it—including the Improved Power Sigil (Krau) feat right in Races of Destiny alongside naenhoon. If you were, say, limited to spell levels you actually have access to with these effects, you’d think they’d say so.
So anyway, let’s assume we can choose any spell level from 2nd to 9th for this casting of secret weapon. Whatever we choose, the spell would be “as difficult to prepare and cast as a spell of its effective level,” so that would normally act as a built-in limiter on the power of the spell—if we choose 9th level, our heightened secret weapon would need a 9th-level spell slot.
Naenhoon says that, as long as we “expend a number of turn or rebuke undead attempts equal to the normal level adjustment of the metamagic feat,” we don’t need the higher level spell slot. By the way, “normal” pretty consistently means “without the current effect we’re in the middle of describing,” so there’d be no need to worry that Heighten Spell’s level adjustment isn’t “normally” any one thing, but is variable—but in this case, remember that Races of Destiny has us double-covered by addressing Heighten Spell explicitly in naenhoon.
So since choosing 9th level for secret weapon would require a 9th-level spell slot, that’s an 8-level increase over its usual 1st-level spell slot. We don’t have 8 rebuke undead uses, however, so that doesn’t work. But we do have 5, so if we choose to make it a 6th-level secret weapon, we can use naenhoon to power that.
So long story short: technically, you don’t expend 5 rebuke undead attempts and then figure out what spell level that gets you; you (technically) choose to cast it as a 6th-level spell and then decide to pay the 5 spell level adjustment using 5 rebuke attempts rather than the higher-level spell slot. Obviously, if you want the highest-level spell you can get, you back-calculate from your available rebuke undead attempts to see what that is, but that’s just how you figure out what spell level to go for, not an actual game-rule choice.
Finally, just a note on alternative possibilities:
- Divine Metamagic (Complete Divine) works the same as naenhoon. Compared with naenhoon, it costs a feat, is restricted to a single chosen metamagic feat, and only applies to divine spells. However, it also doesn’t have the 2/day limit, and doesn’t require us to be an illumian, so those are rather considerable advantages.
- Improved Power Sigil (Krau) is also a worthy consideration—it only heightens by 1 level, but it does so completely for free, which is pretty nice. Plus, krau itself is probably the strongest power sigil, though none of the words it can create are as strong as naenhoon.
- And everything else, that I can find, but since we’re being careful about this I want to correctly identify its spell level as being something particular to each spell list that contains it, and not an intrinsic property of the spell. Another spell list could easily have it as a 0-level spell or a 2nd-level spell and that would be fine.