Re: more religious issues
Aikido the art of harmony is not just a title we can spout whenever we like it. Either you subscribe fully to it or you don't in which case you're probably doing a quasi aiki jutsu martial art.
However being harmonious does not imply bow down to every tom, dick and harry's demand. Instead it revolves around the natural law and a major part of that law requires respect as its back bone. That's why Rei is 1 of the 7 characters intrinsic in Budo.
Rei is sincere respect and can only be given willingly. It can't be demanded nor enforced. However, rei can also be given in many forms. A slight bow does not diminish the heart's true intention or respect in any way at all. Nor does a head to the floor bow actually signifies true respect.
Form outside, ignore. Its the intention that counts.
The sensei may have to appear generalistic in enforcement in what would be something that is difficult for him to do. This is to maintain order. Or he could genuinely feel disincline to blend with the wishes of the particular group. Either way, his intent will translate to his waza. You can sense true harmonious feeling in his waza or not. If you can feel that, then stay on because whatever the outward reason those particular group is excluded, the sensei bears no ill will. If you don't feel it, then maybe you can explore other options.