We currently don't have a way to 'ignore' incoming calls on the Desktop App, while at the same time allow incoming calls to the Mobile app, when they are registered to the same extension.
Your only solution would be to have 2 different Extension numbers:
1x on the Mobile Apps of users and would be for calls.
1x for the Desktop Apps that users can use to chat with, send/receive SMS, etc.
@iMark22
How bout using the webclient instead of the desktop app? You'll still receive the call on of course but it may seem a bit less intrusive as the dialer is not detached and will not pop-up separately.
You might also want to look through our Ideas Section to see if anyone else suggested this as a feature request so that you can upvote the post and help push it up the list!