In short: I feel like my body is being ruined and that my dojo is becoming a cult. I feel fed up and am thinking about leaving but I'm reluctant because of what I've gotten out of Aikido so far.
Many ppl don't like what Chiba sensei is teaching,because they simply don't understand it. For me, sensei is one of best teachers I've ever met, and I had a chance to practice with many of O sensei students.
It is true, some of his students are overzealous, but generally this type of training transforms your body and mind and prepare it to discover a true goal of aikido practice. It will very very difficult, if not possible, to find similar approach out of Birankai. So if you quit now, very probably you will not be able to practice aikido anymore.
Body transformation - it is an illusion to think you can do it without injuries. However when you are young(25) , they heals fast.That is the reason for vigorous training now, Later you can always slow down.
Mind transformation - if I was you, I'd try for longer time those "strange" exercise your instructor is proposing. It has nothing to do with 'sect", it is a part of spiritual training.
I think the key words are 'commitment' and 'sincerity'. You are developing it now to be able to still practice 50 years later...