I had a leak in my roof and now a water stain on my ceiling. My ceiling is not painted. Can I seal the stain with a primer and then cover it with thinned joint compound so it matches the color?
Old question but to answer it...
Yes you can seal it. You cannot use regular paint or it might take 50 coats. You need an oil based sealer to do this right. That will still take 2-3 coats and you will be fine, and then add your paint over it (given it is appropriate to be installed over that sort of sealer/primer - if not you will need a latex prime in between).
There is little chance that drywall is compromised unless it has gotten wet for long periods of time. Drywall is really really good at getting wet, drying and maintaining integrity. The key with water is mold not the stability.