Jordan in Babylon Jones, was already working with her. In Exploitation-Now Jordan probably was under a different name and guise. Renting out her house to hoars for rent and then finally being hunted down By Jones. Jones obviously had bluffed the info about her death. The whole idea of "Pee-pee boy" being given job of boss for that specific area of expertise, wanting to lose his virginity specifically to Jordan, was the reason why she was hunted down ( caught etc ) in the original series. Now that Hooper was in charge again, things would have run more smoothly and logically and thus he did not need her anymore. So it was about just killing her from then on. Not about capturing her.
The facility while receiving government funds ( like Poe and Imps tax dollars ) was more or less working with it's own agenda after accomplishing it's original goal. Think of it as with "Scanners II" and the commissioner and chief had full usage to open a testing facility he kept from his boss. The facility in this case was now back under control of Hooper.
Also they had more brain children, and letting one lose is no big deal. So the bigger question is. Why hunt Jordan now?
Again pee-pee boy wanted her sweet freckled ginger breaded vag ( that never really get any attention and was rejected by the tentacle monster ), or any other super-power, syndicate, or whoever she sold/stole uranium/weapons from. Basically Hooper did not want anything to do with the brain children at all. He brought her back just to get close enough to kill him. So he could purposely blame her.
The whole place and Hooper was blown up ( unless he comes back as Robo-Hooper or RE:V Weskers or something like that, but who would want that ). So now nobody wants Jordan. Asides for those other people, and the Canadian government.