Interesting but I respectfully disagree with your conclusions. Natasha to me is a wisdom based character. Monk/inquisitor most likely. She is uncanny in her perception and manipulation of people while being proficient at ranged and unarmed combat. Ninja doesn't spell that to me.
Inquisitor doesn't fit, since she usually works alone, so she doesn't use the teamwork feats, and has no magic, and monk doesn't fit since she's actually an effective character without going with an archery build.
Apart from her Combat Skills Black Widow is a Bluff/Diplomacy MASTER She is much more a CHA based than a WIS base character. When Ironman was rebuilding the Avengers in Mighty Avengers just after Civil War he brought up Black Widow as a person to fill a Ninja "like" position she also deals in both Disguise and high levels of Stealth Ninja fits just fine.
I'd almost go Ninja/Slayer
I was setting up a Golarion Avenger's Team using She-Hulk Brawler (Mutagenic Mauler), Black Widow Ninja (Spy), Wasp Sorcerer(Fey Bloodline, and Mockingbird (Brawler)
The only reason I didn't suggest the Spy Master for Natasha is because short of a few very specific kinds of games the class is never going to really contribute to the party.
Regardless the point has been raised that while Natasha is a field agent she is much more heavily charisma based. From her looks (which disguise her sharp wits and keen mind) to the fact that she can bluff her way past nearly any door she's a spy first and foremost.
Combat is a necessary part of any RPG however, and it's a necessary part of comic books it seems. The Widow's abilities are best utilized with sneak attack, since she always takes her opponents unawares. That's the primary reason she comes out ahead in most fights; they don't know she's there, and underestimate her significantly.
Part of being a good GM is to include things that involve each of the character's skills and back story. Natasha would have plenty to do in most of my games