To prevent war from breaking out, Hunter and Bobbi maintained their cover and went on the run, denying any and all connection to S.H.I.E.L.D. Coulson had no choice but to disavow them.
Hunter’s return in Season 5 probably means that he’ll either sneak in unofficially or have his sticky situation resolved.
Unfortunately, the manner of their exit meant that they couldn’t simply be brought back into the fold at S.H.I.E.L.D. In their final episode, they were undercover when they got stuck in the middle of a crisis that could have resulted in war between the United States and Russia.