I love disc brakes. Good mechanical discs like the Avid BB7's are just as reliable as rim brakes and have more stopping power and better wet weather performance. Weight is either a wash (if you get disc-specific rims) or it's maybe slightly in favor of rim brakes, but the benefits aforementioned push the needle to Discs for me. All of my bikes (3) are Avid BB7 disc brake equipped.

If you're new to disc brakes, they can seem very intimidating, but 30 minutes with Youtube will tell you everything you need to know about truing rotors, replacing pads, setting caliper distance, and adjusting cables. I can now true my brake rotors by hand using telepathy because I've had a little practice, so I never, ever deal with pad rub. I simply don't tolerate it.

Less than $1000 is a better deal by value-per-mile than almost any other bike in the market since a 9-speed LHT will ride for ever without failing, if taken care of.