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The problem is getting a "mixed" marriage, which does not mean Muslim and Christian or foreign and not foreign but Catholic and Protestant Christian. The Catholic partner needs a "dispensation" to be allowed to get married in a Protestant ceremony (which, as we were told, has never been granted in Malta) or otherwise, it will be a Catholic ceremony, meaning, the Protestant partner cannot join the communion. Otherwise, you could go without the sacraments/mass and just have like a wedding service.
You cannot choose any church to get married in, but there is like a list of possible churches and chapels. "Indecent"  locations are not possible, like at the beach, by the swimming pool, etc.
You need TIME and hand in the paperwork in a special order and timeframe. Make sure you start early enough.
You basically need a birth certificate, a proof that you had not been married yet or are not married at present. When applying, you need to be able to tell the date, name of priest and place / church. Good luck!

Or you have a civil service only, and leave religion out of it entirely, which is what something like 25% of the weddings in Malta are like (very rarely between 2 Maltese though)

Details on civil weddings, from the tourist office