Never thought I'd say this, but I think the .40S&W is perfect for the military's needs. Since no JHP a larger caliber makes a difference and it is decidedly larger than the 9mm. Still, it also keeps many of the 9mm's advantages- not nearly as large as .45acp so both in space and weight more rounds are easily carriable, high velocity and thus high penatration, high cap mags in a reasonable sized weapon, etc.
A second area I thought I'd never be "won" over by, make the military side arm a polymer handgun. You can keep most or all of the strength and ruggedness of steel without the weight. Especially for infantry and special ops types keeping the weight down on any particular piece of equipment is important. I would say something like the Walther P99, SW99, SA XD40, HKs, SIG Pro, and even Taurus 24/7 (if it proves itself a little longer) or a .40S&W version of the Ruger P345 would be just about perfect.
As for availability- the military will certainly supply ammo, if you need to do a battlefield pick up of ammo you can also pick up the pistol from the same source, and if we issue a caliber it will likely become a (if not the) NATO standard quite quickly.