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 1: you can suppress most stuff 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.
Update 2: From today onwards, GRASS 7 now supports your wish (see Changeset 51466):
GRASS_VERBOSE=-1 now discards error and warning messages
The source code is available from the GRASS GIS SVN source code repository or next Saturday as SVN snapshot.