I assume from your description that your index finger is being pinched against the nock of the arrow. If your index finger is pressing down on the nock, in addition to hurting your finger, it will hurt your accuracy by creating a down pressure on the arrow, and the arrow will rebound when you release it.
Sometimes this can be caused by the elbow being too high. Is your forearm in line with the arrow at full draw?
I also switched to using a deep hook on the string, and found that it improved my accuracy. I can tell because sometimes when I start a shooting session, I won't be shooting as well as I can, and as I go through my checklist of all the things I might be doing wrong, quite often I'll find that I've slipped back into the old habit of not holding the string in a deep hook.
I've also found that it's not enough to simply place the string in the first finger joint. I shoot better when I curl the first finger joint around so it's at more of a right angle with the arrow. It's kind of a challenge to keep the back of the hand relaxed when you're doing that, but it does seem to help, and might even help your pain problem as it would move the part of your finger that's hurting further away from the string and arrow nock.