So what's your question, Dan? The bank can't deal with you to do a short sale without the full cooperation of the owner, and you can't get around the agent unless the property goes to the bank at the auction. The agent's rights and commission are protected by his contract with the owner. On the plus side, it's in the agent's best interest to close the sale before the auction or else he looses any chance of getting paid.
I can't imagine what contract you have with the agent unless you contracted with him as a buyers agent. I presumed you had a purchase and sale contract with the OWNER (which does have language to protect the agent, but is primarily between you and the owner, not the agent).
I see your options as:
Buy the house now and pay whatever price you can negotiate with the seller and agent which would likely be the full loan payoff amount plus the agent's commission, plus any of the seller's closing costs.
Hope that the agent is able to get the short sale through. He may be incompetent or poorly motivated, or he may be doing everything humanly possible. Sometimes banks are harder to deal with than the government. There can be so many bean counters, required approvals and signatures, unexplained delays, etc., etc. that it's amazing they ever accomplish anything. You could talk to the agent and ask him to let you be more involved in the process and help him out, or you can track down the owner, get his permission to work with the bank, and try to do the short sale yourself (the agent will still get his commission from the sale).
If either of these options don't work, then all you've got left is the auction or the REO route. If you try to buy it from the bank as a REO, nobody said you had to wait months for them to re-list it. You can send them an offer or start trying to buy it from them as soon as the auction is over (although don't expect them to move any faster then than they are now). Lacking patience can sometimes be very expensive. You decide how much you want the house.