Sanctify Ki Strike applies a straight damage bonus to your attacks; it does not affect the type of that damage in any way. So if you were dealing nonlethal bludgeoning damage (e.g. unarmed strike), you are now dealing slightly more nonlethal bludgeoning damage.
The bonus holy damage from Holy Ki Strike is the same as bonus fire damage from a flaming weapon, which... RAW, your weapon deals nonlethal damage, and the extra holy damage is still part of your weapon’s damage, so it would be nonlethal too, in both cases. But that one is worth running past a DM. There’s really not anything wrong with nonlethal holy damage or nonlethal fire damage (there are even explicit cases of each), but a lot of people find it weird and nix it. But, officially, without a statement in Holy Ki Strike saying “this damage is always lethal,” the choice to use your weapon to deal nonlethal damage would apply to the extra holy damage as well.
The other issue here is that the Holy Subdual feat makes no sense. The bonus damage from smite definitely can be made nonlethal just by choosing to deal nonlethal damage with your weapon (similar wording to Sanctify Ki Strike), and the bonus damage from a holy weapon, RAW at least, should too (similar wording to Holy Ki Strike). So clearly the authors of Book of Exalted Deeds thought these things would, by default, always be lethal. They thought wrong, at least in the case of smite and really also in the case of holy, but nonetheless there it is, in the book. Which isn’t so surprising—Book of Exalted Deeds is a terrible book, and its authors thought a whole lot of things that were completely untrue. For example, the book claims using poison is evil—a position taken by no other book in the entire edition (and completely nonsensical when you consider things like Always-Good couatls and their natural poison).
On which note, I want to address another of the many failings in Book of Exalted Deeds—the vows. The vows are poor fits for the system, conceptually, and extremely poor fits for the system, as far as execution is concerned. Vow of Peace and Vow of Nonviolence, in particular. Please run this character past the entire group (not just the DM) before playing it. This character completely changes the premise and dynamic of the game, for himself and also for the entire party, since the vows affect others. I, for one, would object strongly to having that sprung on me (and have, in the past, dropped out of games in which another player had gone a similar route). D&D 3.5e is not a good choice of system for this kind of character, and the presence of this character could very well ruin the game not just for you, but for everyone else as well. (Judging Vow of Peace/pacifism, not monk.)
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