To dig a little loose soil here, I also think that being able to toggle auto fire (mouse 4/5 anyone?) would be a great feature.
Sometimes spaffing Polaron all over the place is a desirable thing, but when you're in polite company it's best to keep your weapon in your pants.
You can. Either you do it via config files or via the mouse if it's capable. I can press a mouse button and switch between a few modes/etc. The current auto-fire for ground is just what's found in most typical MMOs, nothing unusual or bad about it.
All in all though, I have it turned off always on ground and most of the time in space. Darn command queuing ..