I may be off in my guess of the problem, but it seems to me that the key is more at fault than the starting system...
Before I would make another trip to the dealer, check the owners manual for the sequence taken when changing batteries in the remote...
I can't remember the exact details, but after you change the batteries, you are supposed to put the key in the ignition and turn it to the "II" position and let it sit there for about 15 seconds...this allows the car's computer to read the key and "synchronize" the code.
After doing so, turn the ignition off. If you can open the trunk and doors with the remote, you should be able to start the vehicle.
If you still can't get it started, then you may need to get a new one ($100+). Still, the courtesy keys should be able to work?
I have two remotes for my 95 (one of them is shot) and one courtesy (non-remote) key and one valet (also non-remote) key. All of the keys including the dead remote can start the car!
2009 ML350 (84K) - Family vehicle
2001 CLK430 Cabriolet (71K) - Wife's car
2005 BMW 645CI (124K) - My daily driver
2012 Mustang V6 (60K) - Daughter's car