Your ankles will get used to it, however I very rarely run offroad in anything but low profile heel trail/fell shoes as I find the heel of my road shoes far too built up for happy offroad running, my ankles would always feel vulnerable (I was just coming back from a bad sprain when I first started). Most of my trail runs are hilly and cover a multitude of surfaces including rocks, ruts, roots, grass (usually wet), mud and shin deep bog so I always need the grip and the "trail feel" from low profile shoes. I have a pair of Mizuno Wave Harrier shoes and they are fantastic, the only slight drawback is that the trade off for the low profile is less cushioning which means that long runs on very rocky trails or on the few days when the trails are really dry I can get sore feet, though I still wouldn't want clumpier shoes on as they feel like clogs in comparison.

My ankles are pretty strong now!