The whole prayer garden matter really didn't bother me that much. But while I don't think people should let it feel like a burden to have to see these things, I do understand where some come from when they say that they don't feel as comfortable with these things being on KS. I don't think meeting half way on this or any other matter would really hurt anyone or anything; but both sides need to give an effort here.
I agree with @Aesop
s statement. Prayers are not always religious, and they can mean many things other than praying to one or many gods. It could simply be having hope for one or multiple people, or wishing for the best.
I like that they changed the Prayer Garden, though. It should now invite people of all beliefs who need support. Which, I think, was the only issue with the category in the first place.