I've been looking into this. I noticed the color shift with ffmpeg, and have reproduced it in just about every other quicktime based process, including Compressor, and even Photoshop when it exports with Quicktime. Needless to say, if you spend quality time tweaking your raw color in Adobe Camera Raw, this is the last thing you want. It's totally noticeable and totally unacceptable.
I don't use After Effects, so I haven't tested that. But its Apple counterpart, Motion, works, as does FCP X. X is a little clunky for this sort of thing, but Motion is just about as fast as Quicktime player. No need to even save the project when you're done.
If you export via Motion, the source .tif file and the resulting .mov file look identical. Interestingly, although Compressor causes a color shift when you process image sequences with it directly, you can batch Motion projects through Compressor and the colors are still good. I believe Motion and FCP X use a separate codebase from the older Quicktime apps.
If you're handy with the command line, here's the script to invoke Compressor on a Motion project. Just fill in the blanks for your setup:
/Applications/Compressor.app/Contents/MacOS/Compressor \
-clustername "This Computer" \
-batchname "dngbatch" \
-jobpath "/Path/to/motionproject.motn" \
-settingpath "/Users/yourusername/Library/Application Support/Compressor/Settings/yoursettings.setting" \
-destinationpath "/path/to/some/moviename.mov"
So: Apple Motion. Either on its own, or through Compressor.
