Well, let's face it: she is a person of interest, LE just isn't ready to say she is yet. Were she not a person of interest, they wouldn't have circulated posters with her face on it and give her multiple lie detectors, and they wouldn't pass info to Kaine about her and advise him to seek a restraining order and keep the baby away from her. As I see it, POI is used like "innocent" is used - for instance a murderer may be legally innocent until proven guilty, but in reality he's guilty from the moment he commits the crime. In the same way, someone is a person of interest when LE takes a specific interest in them, even if they are not officially and publicly labeled a POI.
Also we have no idea how much evidence LE has. Clearly they have far more than they're making public - we know this because we only find out pieces of what LE knows far later and through a circuitous route (such as Kaine getting info from LE and acting on it, then reporting that he has done so, with no denial from LE). LE would be foolish to share all of their evidence with the public. KH, DY and TY have all made statements that they know some piece of information from their LE briefings, but are not at liberty to share it. So although WE might not have evidence of wrongdoing, LE certainly could.
Finally, had she wanted contact with her own child and were she innocent, there are legal avenues for her to have followed. Or to follow in the future. Doesn't look like she's headed that way quite yet.