Building a house over a well is a lot more common than you may think. I'm sure you've seen movies or pictures of pitcher pumps in kitchens. I doubt it will cause any more of a moisture problem then what comes up through the soil in the crawl space. Contaminated stagnant water may be a concern. You can always lay a moisture barrier over the entire craw space.

It should be noted that in many jurisdictions abandoned wells must be filled and must be filled in a prescribed way. Check with your local building dept.
Jack