I took my car in last week for the very same issue.
My brake pads are down to 3 mm (WHOOPS!!), as well as a broken Wheel Speed Sensor. The dealership said they wanted to change the pads and turn the rotors for $130 in the front and $130 in the rear. TURN ROTORS!? Waste of money, if you ask me. I'll take my car to my buddy's house this weekend for the pads and just get new rotors when I need to.
I know there could be an issue with uneven wearing, but I really don't think it'll be a major one. It seems to me that they just want to turn the rotors because it's a time-intensive process that they can charge me up the arse for labor.
As far as the clicking in the pedals... I'm fairly certain that's just your ABS freaking out (possibly due to a broken sensor), because mine will do that to from time to time. Basically... if the light isn't on, and I get on the brakes hard enough... they click like that and then the light comes on, and it basically shuts down the ABS. It's basically over-acting, as far as I can tell.
It's the same thing it does when you're trying to stop on ice. It's kicking the anti-locks on when they really don't need to be on. Which is basically the reason that I don't care for ABS... Less control, essentially.
That was a long post. Hope it was midly helpful.