Oh, good point ... Ehhh I dunno, she's a massive flight risk, she came willingly to SHIELD the first time and so far they haven't done anything to piss her off, but they've given her all their info on Loki with the exception of his current location. Without that, she can't do that much damage (unless she plans to smash the entire world to find Loki which is unlikely), but now SHIELD don't have tonnes of intel on Loki that they can barter with. 
I think letting her chill with Dwight and stretch her legs is a good option for now, she may be a little more reluctant to be taken in by SHIELD again if they call her in. 

Right now, SHIELD isn't an enemy or an Ally to her, afterall, Wilson even said that Loki was helping deal with the Hulk and from where they stood, he was more of a hero than she was, but they are aware he could be trouble given his history. So SHIELD don't want to destroy Thor (at least not yet anyhow o-O) and they aren't on Loki's side either (nor against him), so they're at a stalemate for the time being. 

As things progress, Thor and Loki will inevitably cross paths again, and SHIELD can figure out if (a) They can get the two Gods to work together or (b) Who is the best God to become an ally with or (c) Tell them both to fuck off haha or (d) SOmething else entirely who knows where things will do. I think its too early for Fury or Wilson to make the call of whether Thor or Loki can be trusted, since both were trying to help the Hulk situation, and SHIELD doesn't exactly know about Thor and Loki's personal feud, they've only heard Thor's side (and it was very vague -Loki destroyed Asgard ... the end- Give them a little more time.