It's a one-rank demotion, since he was Santo Hei to begin with. The bigger half of it is that it's a big deal to SAINT that their conditioning works as intended, so he can't be an operative until that's resolved. The Ryujo needs infantry, and they have reason to doubt Fyodor can do his job (since he stabbed and blew up the one prisoner the crew managed to take, apparently for no reason---for some, it's even worth considering he might have sabotaged the crew deliberately.) He's effectively on probation.
Since he's not trained as infantry (or as anything other than a SAINT operative), it makes sense to give him a trainee rank for non-disciplinary reasons as well. If it helps put things in perspective, around seven or eight one-rank demotions took place after the battle, along with at least that many one-rank promotions and a few two-rank promotions in addition. No one was demoted two ranks, although one or two crew members might be in the brig. The crew has less than eighty members.