Arduino and Computer Communication
Actually, you have two general options:

1) As I think you are suggesting, you can write some sort of intermediate software on the host system side which translates from the interface the existing software requires to the one the Arduino actually supports.  In theory this should be a great solution; in practice some operating systems may make it difficult to install.

2) The ATMega16U2 USB interface microcontroller is reprogrammable, and the source code for the currently virtual com port firmware is available.  Further, there are already source code examples out there for implementing different USB interface schemes in that chip (most may be aimed more at the Uno, but porting should be trivial)