Just uninstalled the three packages. For gms I got:
FP3:/ $ pm uninstall --user 0 com.google.android.gms
Failure [DELETE_FAILED_DEVICE_POLICY_MANAGER]
and had to go to “Apps for device managment (Security and Location)” first and disable device management “Find device”. I seem to remember that I had already done this… 
I can still receive and send SMS using QKSMS.
Edit.: The section in the settings for system updates is gone! That should be no problem though, when Fairphone releases stock images…