My experience has been that MC has always been far more susceptible to this then any other piece of software I have run on a Mac. It seems even worse with its Media Server running in the background.
I have no answer. My avoidance behaviour is:
1. Limit as much as one can making changes in MC.
2. Use other software for certain things e.g. I now use Yate to do all my metadata changes, and control JRiver as much as possible using a tablet.
3. If I have to go in to MC, I close down any other applications I may have running on the Mac - precious few actually.
Sorry this is not a particularly helpful reply, but I share your pain.