You might be interested in the fact that currently Pokemon Go doesn’t work properly with Android 7 on the Fairphone 2 anyway, regardless of the permission problem you encountered … here’s the bugtracker (you can upvote the issue there to make it more important to fix):
If Pokemon Go is a priority for you, you can downgrade to Android 6 for the moment until the issue eventually gets fixed. See the “I regret upgrading, how do I downgrade?” section here …