Diggin through the pymol startup code, I figured it out! The args list for finish_launching is a direct command-line args list including the executable name (even if this called from a completely different source). So the following works well:
pymol.finish_launching(["pymol","-q","-M"])

Thanks for your response, Jason. 

Cheers,
Derek 

On Sat, Oct 20, 2012 at 1:17 AM, Jason Vertrees <jason.vertrees@schrodinger.com> wrote:
Derek,

    pymol -M

should force PyMOL to use mono even on stereo hardware. Is this not
working for you?

Cheers,

-- Jason

On Mon, Oct 15, 2012 at 5:02 PM, Derek Ashley Thomas
<derekathomas@gmail.com> wrote:
> Dear all,
>
> I am having some strangeness with Mountain Lion and Pymol, which seems to be
> related to desktop switching.
> Essentially this causes flickering and corrupts the entire display until I
> close X11. The problem can be solved by
> opening Pymol in mono mode, but I have some scripts that I want to launch
> from python directly.
>
> Is there any alternative to `pymol.finish_launching()` that can open in mono
> mode? Can it be disabled from .pymolrc?
> Or perhaps I can compile pymol in mono mode. Any attempts at looking at help
> documents and internet searches
> reveal nothing beyond the "-M" command-line flag. I currently do not have
> needs for stereo, so any way to disable it
> would be very helpful.
>
> Any thoughts or suggestions would be very appreciated. Thank you in advance.
>
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, Inc.

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120