I sent my daughter to a church school in Malta and because I'm a single parent I have the right not to pay the donation, now this week the head-mistress called my daughter into the office and requested the donation be paid by force, is this true?

I don't know what the law is in Malta, but in the US any not for profit organization who uses the word donation may not require any money at all.
Now of course this school may soon start finding reasons your daughter isn't a good fit at their school.
This is terrible, calling her in to tell her something that is between adults. They should have called you. You should call them, ask to come in and talk, and be very forthright about your finances.
There's no point in tiptoeing around the subject. Be honest about not just your finances but also your feelings about school policy and church policy and the law.
You don't want your daughter to be caught in the middle and mistreated in subtle ways, if they back off and let her stay. It won't be worth using her to set a principle.