Hi! Thanks for the question!
To get the taxes paid in the last 6 years would not be an option as you should have objected before the taxes' cheques were issued.
If your school is duly registered with the concerned authorities as a charitable issue, you may move an application duly supported with the Registration certificate, PAN Card, ITR and whatever is demanded from the office, before the tax collecting authority. You have to establish that your Sanstha is a non-profit organization.
If you get entangled for the nominal rent that you are talking about, the returns would be difficult.