The time ship wasn't destroyed.
The raw resources used to make the time ship were removed from existence.
Some of the fake science used to make the weapon could have been incredibly rare which might have made building the weapon impossible or just added months to the construction timetable.
Later we discover that a Krenim scientist is inside Seven's brain.
"Krenimia"(???????) seems to have been assimilated before Anorax built the weapon even if that temporal scientist Janeway was talking to wasn't Annorax.