I believe what Pyro, Skuzzy and company mean is that AH2 will replace the current version of AH. Just like 1.11 replaced 1.10. In AH2, there will be two options of play. The first will be reminiscent of what we are currently playing: MA with furballs, base captures, gv assaults, etc. The second option will be the new Tour of Duty, where you register a character and build your military career. The stats are kept, and your Avatar moves up/down in rank and position depending on how well/poorly you accomplish your goals.
So, if you log on and just feel like mixing it up Quake-style in the new MA, you can do so without affecting your Avatar in the Tour of Duty.