As far as I know, there are no c_script commands to set AA and other video card settings.
The fps however should be much higher. I made some tests, where I had more than 6000 visible kps (mostly chunked terrain with multitexture shader), sky, some functions and I got more than 60 fps in a higher resolution (1280*1024 with 4x AA, 8xAF).
So this is strange. Are you using a model instead of terrain. Maybe it´s so large, that this is causing a bottleneck ...?