I had a similar experience last summer.
Dropped a bed on my big toe and had blood building up under the nail. So I drilled a hole in the nail with a hot paper clip. Then ran a trail race the next morning, including a water crossing through not the cleanest water.
Needless to say, my toe got infected, but I kept running on it anyway for about two weeks (was in the middle of marathon training). When, I finally decided to go to the doctor it was very swollen and red -- he ended up sending me to the hospital for IV antibiotics. I ended up having to stay there for 3 days.
After being released from the hospital, I was sent to a podiatrist, who removed the nail. He told me to take some time to let it heal, but that it was up to me when to start running again.
I waited a few more days then started running again. All told (including the hospital stay), I was off from running for just 1 week. Yes, it hurt when I started running again, but was actually not as bad as it had been, now that the nail was gone. By the time of my marathon (a few weeks later) it was not an issue at all.
So if you have already taken 2 weeks off, I would say you would be fine to start training again. Just be cautious and build back slowly. And I would not suggest the "paper clip method" to anyone that might want to try it :)