I agree with Mary, it would just be character derailment to turn her into an Action Girl. However, Irene was not a minor character. She was the female lead from the first movie. By definition, she was minor in the second film, but the death scene MADE her a minor character, she wasn't killed because she was a minor character.
As for a canon justification, there's really very little besides to show that Moriyarti was a total asshole. What was he afraid of? Her not doing her job properly? Fire her. Her helping Holmes to stop him? Does that really justify letting dozens of people in on his murder plot?
I do like that they killed off a major character (which obviously would have to be Irene), but I would have preferred it to happen later.