djay, all very smart responses pain is an indicator something is wrong... thing is... only your doctor can really tell you.
Arthritis can be controlled enough, absolutely- in some cases
In other cases, it will be better once you have lost weight.
The biggest thing, I would say is to stop the c25k- and start working on strengthening your knees. We tend to abuse our limbs, especially the lower ones with the more weight we put on. Let the knee recoup, talk to your doctor and then work on strength training... think of it as physical therapy for your knee. It could honestly just be like ARGH since you've not used it as someone without foot injury would.
Once the swelling in your knee has gone down and you can start walking again without noticing a difference in your gait... the best knee exercise I've found is from someone who was big into holistic practices, and chinese muscle strengthening activities...
stand with feet together, bend the knees slightly, placing your palms on your knee caps, and start making tiny circles with both knees... keep them together and do two two sets of fifteen, one set going in clockwise circles, the other set going counter clockwise... if any part of your feet come up off the floor, you're circles are too big. It doesn't seem like much, but it helps the joints.
Ask your doc about taking CosaminDS Glucosamine/chondroiton capsules... he'll be able to tell you if your body can handle taking it. It helps the fluidity in your joints, helping with arthrities... my father LOVES it. He's up and down ladders all day at 54 with major arthritis
Let us know what your doc says