ThePowerCosmic
Hyped Up
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doesn't mean she isn't freelance. that mission that she was pulled from in the beginning of Avengers didn't seem SHIELD-related. I think her association with the organization has something to do with Barton not killing her.
It seemed SHIELD related to me, and I am pretty sure we are to assume that she's on a SHIELD mission. And so far we've seen her working for SHIELD in IM2, Avengers and TWS. It's safe to say she is fully SHIELD. Her Marvel wikia also mentions her as an agent of SHIELD. Nothing in the MCU so far has said otherwise. I doubt she's freelance.
And yeah, Barton gave her a choice to either come over to SHIELD or die. She chose SHIELD.