My guess is it's because of the Avengers.
So far in the MCU, there hasn't been a threat that hasn't been met effectively by the Avengers. There hasn't been any threat that was shown to be universally dangerous as far as Fury knows prior to the Chitauri invasion. The Avengers were able to effectively combat that.
At the end credits of IW, Fury and Hill were monitoring what was happening in Wakanda. So they knew there was a battle there. When people started turning to ash, Fury must have realized the Avengers have failed and therefore had to call the big gun.
I know nothing about Captain Marvel and what she can do but unless there is some horrible consequence to be paid whenever she uses her powers I don't see why it makes sense for her to stay out of any Avengers-tier conflict, particularly when they cut so close to ultimate defeat.
I would hope her solo film will set up the reason why she couldn't be called upon prior to this particular point.
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