Like most of the posters, I will say that this is a tough call without more information about the specifics of the case. If the child needs so much therapy that his schedule will be significantly disrupted several days a week, he probably belongs in a special program that can truly work with him and accommodate his needs. If it’s a matter of once a week, I think the yeshiva should figure out a way to make it work.
As an aside, a yeshiva needs to remember that they are dealing with Jewish neshamos, which can be r’l wounded or lost because of bad decisions. I know of a family that is somewhat observant and was on the fence about whether or not to send their kids to yeshiva. They seriously considered a local yeshiva that seemed right for the kids and the family and it was all set up until the school informed them that they absolutely could not accommodate the PT schedule of one of the children (who is in a wheelchair). The parents tried to negotiate, move things around, make it work, etc, but the school didn’t even want to talk, they just said no. Did the family send their other 2 kids to this yeshiva while finding another placement for the wheelchair-bound one? NO! The experience was enough to scare them away from yeshiva forever. The kids went to public school and are now not even marginally observant. They have no interest in Judaism and their chances of marrying Jewish are depressingly slim. I don’t think the yeshiva is entirely to blame, but I’m sure they would at least rethink their decision if they could see this family now.