How can I remove web phone links from opening in Google Hangouts?
I'm not sure about removing hangouts completely (perhaps use a cleaning tool such as CleanMyMac, though many users dislike that type of app), but I have a suggesting for changing how telephone links are handled: try RCDefaultApp, a free prefpane which manages default apps for opening different types of files and URIs.

Using that prefpane, you could change the default setting for tel URLs to open using the FaceTime app.

More details on modifying the files that control these defaults are in this answer on SuperUser.