[Carl Elkins] “Regardless of what color space I apply, the colors become incredibly bright and desaturated (even in After Effects)”
The “even in After Effects” comment is surprising. What codec is the source footage, and what effects were applied? Some screen captures would be helpful.
If the issue is purely related to QuickTime playback of H.264 files, you could render using Sorenson or SV3 at full quality and without limiting bitrate. Alternatively, you might be able to play a 720p ProRes or DNxHD file in real time depending on hardware capability.