I think pistols just need decent snap accuracy and/or low TU costs to work well as breaching weapons. "Damage" in this situation is scaled by how likely/often you will be to hit, rather than by how hard you will hit. Having 20% more chance to hit from a 40% snap/auto shot makes a big difference in damage output. It's similar to how the HMG is a great weapon for high accuracy gals, since they can land a few more shots that can make the difference (killed a power armored dude with one!).
The problem with rifles is that they have a weird situation of being both low damage and high accuracy since one usually uses them in situations where you have good odds to hit any ways (crouched aimed shots, autoshot from very few tiles away). So accuracy soon doesn't matter much (there is little difference between 80% to hit and 100%, and no difference between 100% and 160% or you're so close for autoshots that you hit even if you "miss"). That's why a different scaling applied directly to damage would be nice, like it is for sniper rifles (and X-bows which are very similar to rifles otherwise, and one of the most damaging early ranged weapons! but we talked about that already).
Also.. I don't think it would be needed to "nerf" the ranged power of most ammos. A 10% bonus is ~6 damage more for a good starting shot, ~4 more for a bad one, but rifles are pretty weak any ways, so I wouldn't see that as a problem. It might just make melee a little bit less of the obvious early choice.
And that's the funny thing:
You say the advantage is reliability, but for a new recruit, melee is usually the best choice because you have some very dependable weapons (and potentially very high starting melee skill), then it just gets better as skills increase and for high end gals, melee is risky but can produce awesome results.
Meanwhile, a rifle has a harder time to hit, and with lower damage has a harder time to hurt so it is not really reliable, and by the time the gal is good at aiming, she would do better swinging some kind of melee weapon with that big strength she got from secondary xp. Then the only use of rifles is giving gals scoped rifle, for the 140% aimed shot to exploit xp training, increase str and either upgrade to a heavy weapon if she had good accuracy, or more likely transfer her to melee where she can do great damage. (This is for early tech, as you get better guns, that might change, but I'm not there yet.. It's a lot more work to get good guns than good melee).
Re-reading this, I realized, maybe it's just a difference in points of view. I like all weapons to be useful and in the XAE tried to make it so one had reasons to use pistols, rifles and heavies (a bit like the weapons by roles mod, but less heavy-handed) and both gauss and lasers simultaneously at that, so that squad composition looked a bit more army like (mostly rifles, with heavies for support and a few up close specialists).
Now that I am starting to think of Piratez a bit more like XCom-40k (since you said you wanted melee to be where the "heroes" go), maybe the aim is not to give gals rifles (who likes bolters in 40k?!), but to make a squad of melee + heavy weapons, which is actually similar to how army lists are written for 40k (build a melee smashy squad, support it by heavy weapons, minimizes your rifles since they are "useless").
