First off the 9mm AR15 is a gimmick at best, why someone would take a rifle and throw a pistol round in it AND IT STILL WEIGHS AND HANDLES LIKE AN ASSAULT RIFLE and use it in combat is beyond me. There are much better SMGs that fire 9mm or other pistol rounds.
Second 9mmAR-15s are NOT popular at all among civilians. The parts are expensive and its not that simple to take a .223 AR-15 and change it to a 9mm AR-15. Do people have them? Yes, but its not its native cartridge.
I'd much rather have an HK SMG or a CZ Scorpion than an AR15 in a pistol round.
Look, the point is, the one we have now not only fits the game from a balance perspective, it fits it in a theme perspective, too.
Balance wise, the starting rifle is not supposed to be what you want to keep using. As I said before, if you don't have a bullpup, or better, by wave 4, you're either one hell of a good shot with the AR-15 or you have a death wish. The AR-15 is really only any good for dealing with the lower-level trash zeds, and it should stay that way. If it was good for everything (for instance, if it was chambered in a bigger calibre and had a full-auto setting) then there'd be little to no point in investing money in anything below the SCAR.
Theme wise, it fits the bill because the 9mm variant is often used - again - in urban and suburban environments to minimize collateral damage. There are many police and law enforcement agencies that specifically avoid larger, more powerful cartridge sizes because they are so powerful. When it's your job to protect people, it's kind of hard to carry wound a firearm that could easily punch through the wall of a house and kill somebody's aunt in the next room over should you happen to miss.
Remember, we're not out in some sandtrap fighting terrorists who are armed to the teeth with the best in late-war soviet tech. We're fighting in urban Paris, in a training facility, and in science lab. The only guns you're likely to find lying around on the floor, as it were, are going to be weapons used by security and enforcement firms.
Horzine likely has (or had) its own private security force with their own loadout. Giving them a 9mm AR-15 would make sense, because that way they could deal with any escaped or violent specimens fairly easily while still not having to worry about a stray round punching through the walls and plugging their boss.
Simply put, we can argue about this all day, but the devs have given us what they've given us. Personally, I think the twist on what we normally see is a good thing, I like using the AR-15's 9mm variant in the game because we've not seen many, if any, games that have gone out on a limb to use one like that.
Saying we need a full-auto starting rifle in a bigger cartridge would make the bullpup and likely some of the upcoming guns rather pointless.