The thing that cause this problem is not having the brake centered properly so the cam can over rotate and lock up the shoes. Guys who have greased the cams usually don't have the problem, but proper setup avoids it too.
Here is an old post that I wrote a couple of years ago on how to properly set up the brakes.
I did get to work on my brakes last Saturday and get the rear brake properly centered. It's working quite well now. But for you who don't think the brakes work decently on these bikes, Jack took the lead going down San Gabriel Canyon and it's a pretty good long downhill run. It drops from about 6,000' to 2,000' in about 10 miles of fairly tight twisties with some occasional short straights. I got up over 80 on a couple of those trying to catch back up with him. He was going pretty fast, so it was a long time trying to close the initial gap I let him get. He was definitely working me!
Coming into some of those turns and slowing down quickly to 20-25 took some severe braking and I found that the K-70s could definitely be locked up of both ends with the proper amount of pressure. Guys complain about the feel, but I think the brakes offer very good feedback. The harder you squeeze, the more they impede your flow! It's a very linear feeling. They're not going to do 2 fingered stoppies, but you're not going to be surprised by one, either. The braking distance isn't going to be down with a Superbike, but the tires are the limiting factor, not the brakes. You just don't have all the rubber on the ground, nor the tire compound to get all that much traction. But, within the tire limitations, the brakes are all they should be.
As for setting up the rear brakes, put the bike of the center stand, loosen the axle nut, the brake hub nut and the brake pivot nut. That's the one on the brake backplate in front of the axle. Might want to check and adjust the chain while you're there. Do that before you start working on the brake.
Tighten the brake adjustment nut down so the wheel is tightly locked. This will center the brake shoes, and ensure that both shoes are hitting the brake drum when the brake is applied. Torque the Hub Nut, then the axle nut, then the pivot pin nut. Back off the brake adjustment until it is just free so the wheel will spin. You shouldn't have any drag. A couple of notches, (a half to one turn) of the adjusting nut should have it going from locked to drag free rotation. If there is still some dragging a little after another half turn or so, you are probably not quite centered. The brake pedal movement should by quite short between completely free to locked. On the long stock pedal it might need to move a 1/4" or so. My rearsets with the shot pedal is about 1/8". The brakes should be able to lock up the rear wheel, but it will take some pressure, but they will feel better over the whole range.
The next time you have to take the wheel off, take the brake off and grease the brake actuating cam lightly. It will keep you brakes from sticking. There have been a few reports from the iron barrel guys about brakes sticking and breaking! The grease will help alleviate that.
Not much can be done with the disk brakes, other than, of they are soft and take a lot of travel, they probably need to be bled. Those brakes don't take a whole lot of fluid, so I do them from the top. Run a clear hose from the bleeder fitting to a pan and submerge the end in some brake fluid. Put a loop in the hose so you can see if air is pumping out of the caliper.Take the cap off the master cylinder and fill the reservoir with DOT 3 or 4 brake fluid. loosen the bleeder about a quarter to a half turn and squeeze the brake lever. Hold the lever in and close the bleeder, Let the handle out, open the bleeder and squeeze the lever again and and again holding the lever in, close the bleeder again let the lever out keep an eye on the reservoir and fill it before it can get to the bottom of the reservoir. Continue the pumping process until all the air has been run out of the hose.
It doesn't really take too much fluid to completely replace the existing fluid. When you're satisfied the air has been pushed out of the caliper, close the bleeder and try the brake. It should have a very solid feel without a lot of travel. If it has a lot of travel but feels solid, fill the reservoir and replace the cap Make sure the bleeder is closed and remove the hose
To get rid of the excess travel, squeeze the lever very hard and hold it for several seconds. This will push the pucks out farther and keep the lever from having to move so far. Repeat this action a few times and the lever travel should shorten up. This is an exercise I use while sitting at stoplights. Keeps the brakes tuned a bit better.