Yes, ArduPilot does support delta wing aircraft. I just setup one last weekend. Check out this page in the ArduPilot manual: http://code.google.com/p/ardupilot/wiki/AirFrame. There is a section called Mixing Mode that tells you what to set. After you do that it becomes a matter of figuring out the correct combination of setting your Reverse Roll, Reverse Pitch, Reverse ch1, and reverse ch2 for your airframe.
Hope this helps!