If it were I, I'd disconnect the battery entirely from the system. I've done this before. Top up the battery fully with a decent charger before you leave, then it'll be fine and dandy for your return, otherwise you're probably asking for it to fail when it could potentially last a lot longer.
My view would be: The mx5 will be fine, good solid car. Megane - pretty rubbish overall, that's the one I'd be more worried about in terms of ditching it for 3 months.