I have the same problem with my index finger from time to time, the middle knuckle gets sore. I have developed the habit of making an "A" chord just using only my index finger to push down the strings, i refuse to use other fingers because that's how i learned to do it and i'm much quicker that way...(not sure if anyone else makes an A chord that way). After i got a little more serious about playing this year i started to develop the soreness in my index finger you are describing. Instead of totally stopping playing to recover, i just went a little easier on it. Over time i think i have developed some strength in that knuckle and it rarely bothers me anymore.
Another thing...i also taught myself to do some finger stretches and warmups before i play, nothing too aggressive, just to help get the blood flowing better before doing warmups on the guitar. Hope this helps!
