The time ship wasn't "destroyed" it was "removed from time".
Every one on the ship should have been removed form time as well, but i suppose they if the ship was removed completely first, it wouldn't exist any more to remove the crew from time and they would have just popped in the supper vacuum of whatever passes for space outside of time.
the idea of the ship wasn't destroyed.
But the raw resources used to make the weapon, some of which would have been very very very rare, and the loss of which could have put off their time table by months, which gave Annorax's wife time enough to play hide the salami a few more times before the Borg assimilated the Krenim which we discoverd was the final fate of Annorax in what would become status quo for this time during Infinite Recess (And that he's inside Seven.).