Are you sure she knows it's disabled?
As far as I saw, after Joker disabled her implant, the text he sent was just "it's time, come now" or something like that - she came because she trusted him, not because he sent details of what he did to make her safe. And I don't know how much of the details of that might have come up in conversation before they were separated again.
She might not have known that the device was disabled, as opposed to temporarily suppressed. She might not have known, if the device was actually disabled, if Waller etc had succeeded in turning it back on at any point afterwards (at least, not have known until it was too late). So she acted as if it were a threat again, because she didn't have a reason to know that it wasn't.
Also, I recall the team reacting because they're afraid of the bombs, more so earlier in the film - a couple instances of "if he dies, we die" to get them moving, and such. By the time the device is disabled, she has a connection to Deadshot and Diablo, and so comes back and stays to watch their backs and because if Joker was gone, she would have nowhere else to go - and she goes to the final fight because she is persuaded, not afraid. That would cover most of her actions after the implant was disabled, until the very end and going back into custody. That is trickier to explain if she did know the device was disabled, but might be explained by the threat to her new friends (who she does seem to care about by now), the bribe of the espresso machine Waller gave her, and possibility she wasn't sure if the device was or could be reactivated at some point.