So, How will agent of SHIELD deal wit the event of Jessica Jones. It's not like they can ignore her existence, now. At this point she is a known super hero for hire. Nor can they now ignore that people with Mind Control exists, which will make the position of the inhumans even harder.

Yet, it's Shield as well as ACTU's job to catch and grab all the super-powered people. It's not like they can do, Sorry, Hydra solely focus on inhumans, we don't care about some lab-experiment freaks.

Are people going to act as if Jessica is an Alien, as President Kelly said the inhumans were?

It seems, legally, Jessica is covered and is "allowed" to be a powered human without some governmental task force barging in and and abducting her for "security reasons", but that doesn't mean she safe from some Hydra undercover operation.

For anything, I consider the events of the Jessica Jones series happened within a few days and fit between the last week episode of AoS, and the next one, yet I still wonder how it will be addressed. as well as if SHIELD can really pretend they didn't knew about Jessica's powers.

She had to have raised some red flag, seeing she made little effort to hide what she was.