Special Ed services which can be given in the realm of the Yeshiva day in the Yeshiva building is usually accommodated and no exceptions need to be made. However, if a child is going for counseling with a social worker or psychologist the best thing is to not add additional stress to the child by causing the child to miss classes, have a need to get notes, find out the homework and catch up. Having a child fall behind will only complicate the situation.
Therapists usually have evening appointments as well as Sunday appointments. So the first thing to do is to ask the Therapist for available hours and see if they can maneuver another client who is not so time oriented to another appointment so your child can have an after school appointment. If that cannot be done, speak to the therapist to decide whether a different school or a different therapist is the right way to go. Believe me, there are a lot more therapists out there than there are yeshivos that a parent can pick for their child. I would not go to the guidance counselor in the yeshiva to help with this situation because they are paid by the Yeshiva and cannot possibly be as non-biased as necessary.