Is it allowed to pay khums to an institution in which the person is studying/enrolled himself however fee has been already paid.
Along with this, is it allowed for a rich/affordable person to study in charitable institution when there is no other option while at the same time, istitution/uni is not offering full fee programme of study.

If that institution has permission to collect the khums from your Marja then you can give the khums and as you mentioned that fees was already paid.
If there is not any other option then rich person can study in the charitable institution.