Would the Vengeance's Gatling gun and big torpedo launchers really give it much of a tactical advantage?
In the alternate reality, this isn’t a well-developed (or at least, well-known) capability, so you have the element of surprise. As pointed out in the comments and Stick’s answer, by this point in the original timeline, Federation ships already had these “advanced warp capabilities”. But in the alternate reality, they apparently don’t.
For Kirk, the idea that you could be pursued at warp speed (let alone attacked) seems impossible:
Carol, we’re at warp; he can’t catch up with us.
Cue something big, dark and scary catching up with them. Indeed, the only reason that the Enterprise isn’t destroyed in seconds is because Carol Marcus and Scotty are both in the right place at the right time. If you were attacking, say, a Klingon vessel, then that’s unlikely to save them.
When Kirk and Spock talk to Khan in the brig, he acknowledges that the course of Starfleet development changed in the alternate reality:
But as a result of the destruction of Vulcan, your Starfleet began to aggressively search distant quadrants of space. My shift was found adrift; I alone was revived.
We’re told earlier in the film that Starfleet confiscated Scotty’s trans-warp beaming equation, and then it ends up with Khan (who’s also working on their top-secret weapons projects). It’s easy to imagine that warp-capable weapons systems were likewise kept secret, so that you can use them for surprise attacks in a war. That one explanation for the discrepancy between timelines.
(And if you kill anybody who witnesses these weapons, then it’s a pretty easy secret to keep.)
In the original timeline, where everybody knows about these weapons and takes appropriate precautions against them, perhaps it’s not much of an advantage. When it comes as a complete surprise to your enemies? Maybe more so.