^Without going to far in to this, she did a lot to avoid being hit. That's my biggest problem with scenes like this.
Martial arts training does not change basic things. It does not change the fact that taking a punch from someone that much larger than you, especially to the head, is going to do damage.
What Natasha does here is avoid getting hit, which neutralises her larger opponent's key advantage, and uses attacks that are designed to take out her opponent as quickly as possible. She wins by being faster and smarter than her opponents as well as distracting them with various devices at her disposal, nothing I have a problem with and certainly true to the character. Alias was a show where they did this well too.
In other such sequences, you end up with the smaller opponent taking punches and shrugging off attacks from much larger opponents - a good example is the fight in Dollhouse's "Man in the Street". Echo is somehow magically able to take punches that would outright kill her in reality. It's those kind of sequences that ignore obvious differences between opponents that I find ridiculous.