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There is a discussion about the handler of the tel tag here: https://productforums.google.com/forum/#!topic/hangouts/ItliGvezjdM
However, no solution was proposed to make hangouts handle all such tags.
I looked into the chrome protocol handler settings and could not find such a setting. I also attempted to reverse engineer the gmail source code to find out why tel tag is taking me to the hangouts, but I got nowhere. Any pointers will be greatly appreciated.