Illness marked as "less active"

My son has been sick for a few months with mono, and hasn't been able to attend church and activities. Other than and before that he's been very active, and strives to attend his meetings even though he hasn't been able to recently.

Today he went for a temple recommend interview and to seek an ecclesiastical endorsement to apply for a church school, but the bishop said that he "doesn't know" my son anymore and can't give the endorsement, and that he was stretching the guidelines to even give my son a temple recommend because my son is marked as "less active" because of his recent illness. We told the bishop that we feel like he's punishing my son for being sick, but the bishop says he's "just following guidelines".

Is there a way to be marked as "ill" instead of "less active" when prolonged sickness prevents regular church attendance?