If your budget is $2000, you'd blow the entire budget on the camera itself.
You certainly need some sort of audio gear in addition to the camera. For documentaries, lav mics make a lot of sense. As Alcove mentioned, you don't want to mount the mic to the camera, if you're going to go the shotgun mic route, put it on a boom and have someone (preferably someone with experience) operate the boom.
What about other supporting gear? Tripod, for example? Do you already have one? Do you already have a _good_ one?
For lower light performance, you'll likely want to look at a larger sensor camera. Though I would strongly suggest you reconsider that desire for low light shooting and actually light your shots whenever possible.
On a $2000 budget, my suggestion would probably be something along the lines of this:
Sony NEX 5 ~$650 (amazon) (Note: This has virtually the same sensor as the FS100, quality and performance are pretty great)
Tripod with good fluid head ~$130 (
amazon)
A basic LED camera light ~$30 (something like
this)
A basic 3 point light kit
Then spend the rest on audio gear.. including a recorder, for example the
Tascam DR100
This would get you a very basic setup, but with high quality audio and video capability, AND lighting. Obviously you could easily spend more than $2000 on gear, but you absolutely should stretch that a lot farther than just covering the cost of the camera alone.
