The problem with trying to recreate such a character is that Kusanagi is extremely complex. She's very good at numerous different skills: Martial Arts, guns, hacking, leadership, and acrobatics.
I think if you pay close attention to the various shows, she actually doesn't do very well in melee combat unless she's completely manipulated the situation to her advantage. In most cases she's going up against foes that are larger and stronger than her, with all sorts of physical augmentations. If you pay close attention, you'll see that her agenda in melee is not geneally to beat a foe into submission, but rather to get close enough to hack them, using acrobatics and cover to avoid being hit until that goal is accomplished. In almost every case where cover, concealment, and dodging fails, she takes tremendous damage to her cybernetic body.
But at the same time, I hesitate to suggest going with either of the two gun-based power sets. While Kusanagi is extremely good with firearms of all types, it's generally a last resort, or more importantly, a tool for manipulating the enemy. It is not actually her primary theme, which is what would happen if you took pistols or assault rifle as your primary power set.
If anything, I'd say that you'd want to probably go with the Mastermind archtype and choose either soldiers or bots. You'd have some gun-like abilities. Maybe name the bots Fuchikoma and Tachikoma, or give the soldiers names based on her Section 9 squad. The secondary support power set presents some problems, since MM doesn't get any power sets that really fit the overall themes of Kusanagi. Traps would be the closest, I guess. But even that's not really up her ally. I suppose there's a case for time manipulation as a form of "hacking"....but that feels like a bit of a stretch to me.
But I also think that the Huntsman suggested above has a lot of merit, assuming you want to focus on the combat aspects of The Major, since the hacking elements aren't easily represented.
Just my 2-cents.