Is the realtor doing the loan? No? Then ignore the realtor when it comes to the loan.
No one is going to steal your earnest monies. It is YOUR money.
Get your loan officer on the realtor about repairs... you likely cannot close until they are done.
The refund comes from the title/escrow company. You'd only get a refund of the appraisal fee if the seller is agreeing to pay all of your closing costs though.