A good trick to prevent this is to set your microphone to an aggregate device that you create with the Audio Midi Device tool that comes with your mac.

Open that, and create a new aggregate device with just the system microphone. Then set that as the default microphone. And now when applications access the microphone for whatever reason, your bluetooth headphones don't switch profile and keep on using the aggregate microphone device.

It's one of those obscure hacks that should just be default behavior. Why would I want to switch to a low quality audio codec when I have a perfectly good microphone in the laptop? Answer: I don't want to. Never. Loads of people use expensive headsets and they all sound terrible when they take their calls. It's not necessary.