Definitely. This is pretty important to me, and I am sure a large percentage of people. Adding unique remotes (such as the bluetooth remote of the Fire TV) brings us back to the days when each device required separate controllers. I have standardized on Harmony remotes for years and have perfectly programmed remotes for each of my TVs/devices. All other remotes are in a drawer.
I love my Harmony remote too, and would be really upset if it lost the ability to work. It is an "old style" IR-only remote, so I'm already living with it not being able to operate our Fire Stick.
That said, the latest Harmony remotes
do operate Fire Stick and FireTV boxes over Amazon's Bluetooth-based connection (ex, see
https://support.myharmony.com/en/harmony-experience-with-amazon-fire-tv ).
If Apple allows them to, I don't see any reason why the same Hub wouldn't be able to control an AppleTV, albeit with some software and firmware updates required on the Hub/Remote side. The click-button "simple remote" probably won't be able to do the trick, but certainly the smartphone app should. And, once the Hub works with the AppleTV, I'd definitely see Harmony putting out a higher-end clicky remote with touchscreen to control the AppleTV just as the Apple remote did.
Now, though, the motion stuff is all fairly unique, so I'm not sure if Logitech would even want to go there (it depends on if the motion sensitivity is used only for games and the like, where Logitech does not want to replace game controllers, or for basic system navigation, which is directly in the Harmony's wheelhouse).
In any case, I don't think it is wise for us as consumers to require control systems from the 1970s to limit what devices in 2015 are able to do. We do need to move on. I just hope that Apple has learned the remote-hell lessons from the 1970s and 1980s and will at least cooperate with others in allowing universal control.