1) It's not the "only alternative". That's just silly.
2) Actually, last I checked, .40 S&W > .45 ACP in terms of price.
3) You can't use JHP (Hague Convention) in war. If we could, they'd be using 9mm in JHP and they wouldn't need an alternative.
4) More lethal is a joke. Lethality comes first from accuracy. And the difference in cost for the civilian market between 9mm and .40 S&W isn't worth the very few percentage points of claimed "lethality" it presumably has. Take a look at the link below.
http://www.buckeyefirearms.org/node/7866
Honestly, if they want something that hits harder (all other factors being equal, and especially since this is going to be FMJ) but still fits in a more compact grip, .45 GAP. But lethality comes from accuracy first, second (due to military environment and being limited to FMJ) from how large a hole you punch in them.
The above stats from soldiers who express their gripes are mostly not even worth evaluating because they're only opinions. Again, I've spoken with several USAF who have engaged enemies with their M9 in combat and they came away with an appreciation for the gun because it is lethal when they aim.
Really, the limit is Hague conventions. If we can get them to re-evaluate hollow points and approve hollow points that are guaranteed to 99% of the time not separate into individual pieces (which was their main gripe, the humanity of the round), this would be a non-issue, and 9mm would continue.
But even then, on top of this, the logic of depending on any handgun in combat is silly. You'd want your rifle first, as they have more power and more range. The M9 is supposed to be a backup in a combat zone.
My vote (since any ammunition is going to be mass produced by the military through contract, thus making any round cheaper) is .45 GAP. Widest bullet in a compact grip.