The best solution is to use software other than iTunes if one isn't dependent on it for some reason. Many software packages offer Airplay if that is important.
I have most of my library in FLAC but a good portion in AIFF. AIFF is a nice solution all around if storage and transcoding isn't a big deal. I own all the "audiophile" suites and use Audirvana the most when I am at my computer at home (with iTunes integration). When interacting with my main system, I usually use Media Centre and at work I use Decibel (simple, fast and functional).
Each solution permits FLAC but no seamless FLAC integration with iTunes. The seamless adjective is important. All the solutions above offer work-arounds (or in some cases just better software outright) but iTunes is a slick piece on a Mac. It really is tough to beat if one's music is ALAC or AIFF.
Transcoding seems like the best option frankly. ALAC and AIFF can be played on almost any system using a wide variety of players. Using XLD to convert FLAC to ALAC or AIFF and delete the FLACS in the process makes the entire endeavor very painless. XLD also offers the ability to add music to iTunes after each file is parsed.
