If waiting for the lossless audio is the only thing delaying this release then, in my opinion, you should go ahead and release the mkv.
Anyone who is enough of an audiophile to care about having it lossless will know how to mux the track with the video if you make it available later. And of course I'm assuming you're still planning a BD release, so you could always hold that off until you have the lossless track and make it the definitive 'whole package' release.