Does the queen have to eat the entire organism for her to take proper traits from it, or is one bite all she needs?

If she needs to have a good serving (1+ organism?), the ants were probably too small to really give the queen enough food. Remember that the queen can't move around, so the little tiny ants had to carry the bits of food to her. If the entire species was tiny, then there could have been minimal harm.

If they were some species that was isolated to one island with the only other food being fish/random rodents/insects, then their harm would have been localised. It would have also delayed their discovery.

I just hate these all-assimilating beings though. They scare the hell out of me because they're clearly superior in terms of survival. They also just generally don't give a fuck in general.