BW and Hawkeye were good at fighting the aliens because they were both elite assassins, they were top-tier military personnel trained and honed to do these very things...
No, BW's handguns were one of the very few issues I had with the movie. A 12 second scene where Stark whips up a "repulser pistol" in the helicarrier lab and tosses it to her, and her combat effectiveness suddenly needs 100% less suspension of disbelief.
Her physically taking out the aliens and appropriating their staff-blasters I was fine with. That's your highly trained agent. But there's no difference between her 9mm and the one's the cops have. If her two pistols could do that much damage, then a squad of, say, Navy SEALS would have taken out the entire army of Chitauri foot soldiers in half an hour. It is the one thing that makes the Chitauri look completely defeatable.
Her pistols gives us a real life benchmark to measure the Chitauri against. That's where it goes wrong. Cap's athletics and Hawkeye's arrows are off the real-life scale and we can imagine them to be as powerful as the plot requires. A 9mm is always a 9mm.