So this appears to have been fixed with 10.11 El Capitan.
I called apple, got a hold of a great Tier 2 rep, and we worked pretty thoroughly with this issue. Did some extensive process of elimination, even tried the same RAW pics in a trial of lightroom, and they looked fine. Removed and re-added the file aperture uses for raw conversion, same thing. Finally just decided to reinstall OSX Yosemite - over itself - and believe it or not, problem remained. All raw pictures from my a6000 would go random-haywire graphics.
Couldn't get anything to work, but was determined that it was a software issue still, so the tech took this thread and our testing up to the engineer team. That was last I heard.
Yesterday, I did the software update for everything FIRST (including aperture), and the problem remained.
Then, I decided to upgrade to 10.11 El Capitan, and low-and behold the problem is -gone-. RAW pics from the a6000 look absolutely fine now. FIrst time it's worked in months - and only after going to 10.11 (not any other updates). Now... I can't say why this happened, or why an update to 10.11 was required... but, hey, it works, and it was free. Shout out to the rep for helping me out and pushing this through to the right people.