if the mold is blue or white I wouldn't worry about it. But I had a cheese crack a while back and did the vinegar and salt thing which helped with the black mold. I scrubbed furiously too. Later on in the aging the blue and white came back and moved into the crack. The cheese is delicious.
There are some famous cheddars (Neal's Yard) I've seen that always seem to have some blue running through cracks, and they're wonderful.