I'm not aware of any ways to locally override the group policy, although I haven't looked into it much myself. I also looked into seeing if there was a header or something we could add into Mattermost itself to force compatibility mode off, but the best I could find with the group policy enabled would force it into IE8 rendering mode which still probably wouldn't work.
If you happen to find a good way to solve the problem, let me know and I can get it included into our documentation.