It's pretty clear that Burnham was very much against using the creature to operate the spore drive once she realised it was hurting the creature. The continued use of the creature is probably going to be a cause of conflict between Burnham and Lorca, In fact, having to use a living being to operate it is probably going to be why the Federation does not continue to use it.
This is why I'd probably be a horrible strafleet captain. Cause in my head this is simple.
Immoral? yes. But one creature's pain = hundreds of saved lives so far, more potentially in the future?
Won't sleep well but can't say no. Easy decision if not heavy.