Looking at how they ran the Nokia deal and nearly ran the Nokia acquisition into the ground, I have grounds to be skeptical ... but MS has deep pockets and can afford such screwups, most startups can't.
Considering their new business direction which is getting their software on all devices (even non-MS devices) instead of trying to force complete MS solutions down your throat (which not too many people are comfortable with), I think this is an important acquisition for them in order to get their products out on other devices more easily.
So in my opinion, if they screw it up, it'll hurt them in the long-run (assuming they are planning to use it to ease cross-platform development of their Office365 and similar applications) and considering all the effort they are putting into making .NET more appealable to developers, screwing up Xamarin will simply be a nail in that coffin - so they have plenty of motivation not to screw it up other than monetary factors.