In C, a warning message can be suppressed by G_suppress_warnings().
http://grass.osgeo.org/programming7/gis_2error_8c.html#a85673d5f53237ae1c016abcc215871c7
I'll verify how to do that in GRASS-Python.
Update: you can suppress most with:
grass.run_command('g.gisenv', set="DEBUG=0")
but DEBUG=0 will not suppress warnings. So for the GRASS GIS version you have there is only one way, to discard stderr. We'll make it more elegant, hopefully for version 6.4.3 and later.