@CJ1145 That first gun ever was designed with the use of the Apple and as such it can involve technology from any time period, it's just manufactured in the 15/16th century.
You raised the point about it being a setting that Ezio is not used to; Although you are right that Ezio hasn't fought in a jungle in any of the games (I don't know about the comics, etc.) Ezio would be more than capable of concealing himself. You are also only half-right about Ezio hiding in the crowd; Ezio is nigh on undetectable in a crowd, but he has shown an amazing ability to hide without anyone other than the lookout guards nearby. He has even hidden himself from people that are paranoid and always on the lookout for him.
Ezio's main skill is crowd-stealth, as opposed to general stealth. He's good at it, sure, but it's not his forte, and it's more likely for him to slip up in the jungle. And he's never that quiet, if anyone's listening for the slightest sounds of movement they'd notice him coming a mile away.
Wait, Apple? His gun was just a schematic from Altair's Codex (which was supplemented by the Apple, of course). It's powerful, but don't forget the gun was 500 years ahead of its time when Altair even thought of it, then there's the matter of degradation through succession. Altair would take the schematic from the Apple, and get it mostly right but with a few errors. Don't forget, Altair probably doesn't even know what he's making the schematics for, so it's not as efficient as it could be, most likely. Then Leonardo gets it, and follows it as exactly as he can, but you must remember that even he doesn't know what a gun is, per se, so his adaptation may have a few more errors.
The gun is powerful, as the end result, but is also short-ranged and takes a while to aim. It's also extremely loud, so if he missed that first shot, or Armstrong survived, there's no way he'd remain hidden.