I was running the student version of R2012a before updating to Yosemite and was greeted with the "You can't run this application on this version of OSX" after the update. Fortunately, after trying a few things I was able to get MATLAB up and running again. This is what I did that I believed fixed my copy:
-Re-installing XQuartz. I'm tempted to say this is the main reason why older versions of MATLAB are running into the issue as, after trying to open MATLAB in terminal, my computer indicated that the X11 files were missing after the update to Yosemite.
-Installing the most recent version of Java on my computer. I'm not 100% sure this is mandatory for the fix, but I did update Java after the update and a lot of people are noting that this was necessary for a fix.
I can't say I've tested this fix enough to know for certain that this solution will work in all instances, but my version is working fine now after doing the above. Best of luck!