Ok, so if you don't have LEDs, then I would lean towards the brake light switch as others have mentioned. When I used to install remote starts and alarms for a living, I would sometimes come across trucks like this. I think I dealt with 4 or 5 of them over the years. The brake lights actually worked fine and functioned normally. But for some reason there is a slight amount of voltage backfeeding on the brake light wire at the switch. It was enough that the remote start sensed it as the brake pedal was being depressed. Most of them I turned them away and told the customer that I could not install it until they get the brake light switch fixed. One of these was a friend of mine and I basically rigged up a relay to the brake light switch to completely isolate the brake light wire from the alarm. So it didn't see any voltage at all until the brake pedal was depressed and then the relay was triggered. It actually worked great, but he complained that he heard the relay clicking EVERY time he pressed the brake pedal. I told him he could either deal with the relay clicking, or do without the remote start, or else replace the brake light switch. I'm not saying that this is your issue, but I was just telling you the story of my experience dealing with this issue. So that being said, a relay would not work in your situation because you are not adding an aftermarket accessory, the cruise control is already part of the vehicle and no real easy way to isolate it. So I would try another way to test this theory. If you unplugged the brake light switch and it IS your problem, then theoretically the cruise control should work with the brake light switch unplugged. But be warned, driving on a public road with no brake lights can not only get you a ticket, it's actually dangerous. One more way would be to wire in a toggle switch and basically shut it off instead of unplugging it. But I have no idea how the cruise control senses the brake lights. You might need to wire every wire to a toggle switch instead of just the actual brake light wire.
Have you metered the brake light wire to see what the voltage is when the pedal is depressed, and what the voltage is when it's not pressed down? That's actually where I would start.
