I think you should be able to get rid of Google apps by simply re-installing the Fairphone OS through the Fairphone Updater App.
As you can understand by reading my posts in the [“Stock Android (AOSP) Experiences”][1] thread, my experience with going back and forth from Fairphone OS to Stock Android makes me think that simply re-installing Fairphone OS should, unlike a factory reset, reinstate the default configuration without losing apps you might have installed.
This operation should, however, revert to their default some customizations you might have done to the Fairphone Launcher (like background and icons or widgets on it), but it should only be a minor hassle compared to reinstalling everything from scratch.
Anyway, read carefully my posts in the other thread to get the idea of what I did and experienced and keep in mind that I am simply inferring that the method I suggested will work, I’m not warranting anything. 
Backup everything anyway before doing anything.
Bye.
[1]: Stock Android (AOSP) Experiences