Vow of Non-Violence and Vow of Peace have both been violated and should both be removed.
According to Dungeon Master’s Guide, prestige class requirements must be met only to take the 1st level of a prestige class. After you have taken the 1st level of a prestige class, you not only keep class features if you lose the requirements, you also retain the right to take more levels in that prestige class.
And then on Book of Exalted Deeds page 49, the beginning of the prestige classes chapter, we have
A character who ceases to be of good alignment or who willfully commits an evil act loses all special abilities and spells acquired in this prestige class, and may not gain new levels in that class. She may regain her abilities if she atones for her violations (see Sin and Atonement in Chapter 1).
This suggests that the authors were aware of the Dungeon Master’s Guide rules and knew they needed to provide rules for “falling” from these prestige classes. But they only address alignment—not requirements. If killing this orc was not an evil act—which can easily be the case in Dungeons & Dragons—then by these rules, there is only a violation of the relevant vows, not an act that triggers falling.
The apostle of peace itself makes no mention of ex-apostles, no code like the paladin, etc. The section of chapter 2 on “Waging Peace” discusses only how to handle XP in a game where a player or players are not killing things.
Which basically leaves us with one question: is violating a sacred vow itself a necessarily-evil act? If so, then the apostle of peace has violated the rules on page 49 and loses all class features and cannot take more levels in apostle of peace. As indicated of page 49, the Sins and Atonement section on page 20 addresses this situation, and suggests that along with the atonement spell, a penance is usually appropriate in these situations. However, in the case of intentional violation, Vow of Peace and others say the feat is lost irrevocably. This suggests that no penance is sufficient to atone for this, and that would probably extend to the prestige class.
But nothing explicitly says that breaking your sacred vows is an evil act. I would not ordinarily think it is—a non-good act, certainly, but that falls short of being actively evil. Rather, I would think that the oversight is in the blurb on page 49, which should address vows explicitly in my mind. I would say that the list of transgressions that triggers the falling should be
ceases to be of good alignment, willfully commits an evil act, or violates a sacred vow required to enter the prestige class
Furthermore, nothing explicitly says that the “irrevocable” nature of the loss of prerequisite vows extends to the prestige class; that I would also see as something I’m seeing implicitly and my preference would be to make it explicit.
Ultimately, though, I would consider this a houserule, and would likewise consider a ruling that violating a sacred vow is an evil act to be something that should be brought up before a character takes any sacred vows. And since someone playing an apostle of peace requires a lengthy discussion with the entire group of what that means and whether or not people want to play that kind of game, it really should have been addressed long before there was ever an apostle of peace in the game to kill any orc.
At this point, I think the apostle of peace should lose their powers and not be able to continue progressing the class. If the player protests that they thought they were safe to do so under the rules, you should apologize for not spelling it out ahead of time—but not actually back down, because frankly the spirit of the rules in Book of Exalted Deeds is quite clear on this point. It is an extremely legalistic reading to come to the conclusion that apostle of peace features would remain available after violating the vows, and Book of Exalted Deeds is not a legalistic book. If the player no longer wants to play this character under that reading, then you could easily make the character’s penance something that takes the character away from the adventure and thus easily explain their absence, and look for an opportunity to introduce a new character. Your game will be much improved by not having an apostle of peace in it. If the player instead wishes to ret-con their decision to kill the orc, that could be discussed with the group, but unless it literally just happened, I personally would be strongly opposed—and even if it did just happen, I would be strongly reticent to allow it.