I am a mac user and have never been able to get pymol to open in stereo mode without crashing my computer, unfortunately. I suspect that apple is either no longer supporting stereo graphics or they're drivers are messed up on recent OS builds. At least this is the case for all iMacs and MacBookPro's I have used in the past couple years. This means that writing programs that rely on pymol need to watch out and explicitly turn off stereo, but this is not a good idea because there may be users out there that want stereo enabled if their hardware supports it. So, I threw a quick patch together that forces pymol to open in mono mode without the "-M" flag unless the user explicitly uses "-S" for stereo. You can get the patch here:
It is designed to be used on the installation directory, but it could also be applied to a pre-existing pymol installation. Hope this comes in handy to anyone out there.