New pads for sure. Make sure to clean up them calipers good while you're in there. My rotor looks about the same and there's no issues. It's a little scary doing brakes at first but it's not so bad once you figure it all out. Do 'em one at a time with a ride inbetween so if you do manage to muck it up you have at least one functioning brake.
The only problem I recall while changing the brakes is getting the pistons to move back down. I didn't realize it'd take that much force and I'm not a very strong guy. I thought they might've been seized up or something.
http://faq.ninja250.org/wiki/How_do_..._brake_pads%3F