We ran into the same issue. When we were doing weekly counseling sessions, I set the sessions during elective periods at school. That way he didn’t miss important instruction periods but did get the counseling sessions. Late mornings had a time where the class had recess then computers then elective (Art or PE). I was lucky to find a therapist close to the school. And we scheduled his individual special education time right after the elective time. So if the session ran long he would return to school and go to the special education room. Special Ed teacher was able to still give him one-on-one attention while also giving him a little transition period to get back in the groove of the school day.
This was the least disruptive schedule we were able to find. And since his special ed teacher understood that therapy was highly important she was more than willing to help him get through his day. Even though it was somewhat disruptive and he probably did lose some important time at school, at that point, counseling was a top priority. His ability to learn was greatly improved by the therapies, and since he was going for anxiety issues – his overall well-being also was greatly improved.