It is a pity for me to read about all the issues with fdroid, as I really love fdroid and I'm really loving your app too. I discovered the app through the 0.7 version posted in f-droid and have since been following the development.
Both the f-droid version and the latest beta build work great on my moto e 2015 on android 5.02.
In case, you were not aware, f-droid allows anyone to create their own f-droid repo, allowing control of the signatures and the release schedule... It would be best in my opinion if there was a simple way to resolve the issue with the f-droid guys directly but it's true that updates done through their build system are likely to be less timely. In anycase, perhaps rolling a netguard f-droid repo would be an adequate compromise to support the f-droid users?
I'm obviously biased wrt f-droid support but I was wondering if you had considered the possibility of the app being excluded from the playstore once it becomes popular as it can be used to interfere with advertisements shown on the device. From what I understand of changes to marshmallow (if I am not mistaken) all apps are now automatically granted internet rights. If this is indeed the model being followed I could see google eventually having issue with publishing your app on the playstore.
I wouldn't want to jinx anything, and I hope it will be easy for netguard to be supported both by f-droid and google playstore since it really is a great app!.. Just a couple of thoughts.
edit: forgot to mention that if you really dont want your app on f-droid you can just ask them, they have obliged other developpers with similar issues I believe. I really hope it does not come to that though