Yes and no. I am sure, I've said it before, but once again...
It is quite simple: Only Blu-ray players detect Cinavia, so removing Cinavia makes most sense with ... Blu-rays!
So if you want a Blu-ray copy with menus and all this stuff (I wonder why anyone would want that, but anyway), you must decode the audio, remove Cinavia, reencode the audio.
Here's the problem - you need True-HD /DTS-HD decodes and encoders. Not an option. So you'll end up with AC3 (Dolby Digital) sound. LPCM wouldn't fit on the disc.
So it is very simple: You keep the audio quality with TrueHD / DTS HD / Atmos / whatever with Cinavia, or you'll get AC3 without. Pick your poison.
With Media files like mkvs, it would be possible to keep the audio quality using a different codec like ogg, but with media files nobody cares. That's why pirates are not affected by Cinavia at all. Cinavia has no impact on downloaded content at all.
I personally don't care about Cinavia. Thanks to AnyDVD my PCs are immune, and media files are watched with a media player or some XBMC/Kodi variation.
Other people might be bothered by Cinavia, but there is no and there will be no way to remove it and keep the audio quality on a Blu-ray disc.