How do I get my mortgage loan approved if the appraiser declared the house uninhabitable?

I currently have a contract on an as-is house that needs a new roof. The roof leaked through to the ceiling in one small (2' by 3') area, so the appraiser said the house is uninhabitable. Therefore, I can't get the mortgage until I fix the roof and the ceiling. The estimates to do patch jobs on both are about $500 each. I know that I need a new roof and a new ceiling, and intend to replace both as soon as I close, but I'm definitely not going replace both before I close. It would be much more cost effective for me to find some way around the "uninhabitable" appraisal, and do the ENTIRE roof, and ENTIRE drywall ceiling, since both will be ripped apart within a week after I close. If I do patches on both, it'll be $1000 for nothing. I'm trying to get an exception through my loan officer, but I'm not hopeful it will go through. Any suggestions? How closely does an appraiser look at the roof and ceiling? Can I possibly nail a piece of plywood on the ceiling and a couple shingles on the roof? Or will he check for that?