Well, you could say that it works this way, but it's not how other effects in Dominion work. All effects that have the same timing are queued up simultaneously, then you choose which order to do them in. So if the only two Victory cards in your deck are two Wartorn Provinces, you'd end up trashing both of them. Trashing the card the effect is written on doesn't stop that effect from taking place if it's already been triggered.
Interesting. So I guess if I want it to work the way that I thought it did, I need this wording: At the end of the game, if this is in your deck, trash a victory card. Would that work? The first card's effect resolves, seeing that the first card is in the deck, and the player chooses to trash the second card; then the second card's effect resolves, seeing that the second card is not in the deck, and does nothing?
I don't think this would work. From my understanding, "if this is in your deck" would continue to be true and thus require you to trash more victory cards as long as this is in your deck. Or maybe it's not like this. Since there are no cards like this in Dominion, you had best, as Soulnet wrote, write a rules clarification note or a paragraph on how exactly end-of-game effects are resolved. By the way, I like Fragasnap's idea for this concept a lot:
I've played around with effects like this. I call them End cards (so creative, I know). At the end of games, after putting all their cards together and before counting their points, players separate all the End cards from their decks and then take turns resolving them one at a time. I hadn't playtested enough to get to handling adding and removing End cards from players' decks during this process.
I think you can do some very interesting stuff with this. So keep on thinking and share your ideas with us