To answer your main question, yes you have to work with the agents. Both parties signed an agreement and that listing is assumedly protected for a specified time after the agreements end. Land contracts are tricky - why would either of you not want to use Realtors?
There are a few things that can be done. First, you didn't mention what the deficiency was between the agreed upon sales price and the appraisal. Yes, getting a second appraisal can work. Did either agent pull comps and meet the appraiser at the property? If the deficiency isn't tremendous, will the seller reduce the price some and can you come with some extra money to closing. If you want to do a land contract, you will probably have to put a significant amount of money down, probably as much as the purchase down payment if not more.