SHIELD, like any other government intelligence agency, has done a lot of questionable things in the name of the greater good. Were their intentions malicious in bringing Pietro back? Certainly not. They wanted to learn more about HYDRA and the Chitauri technology that Strucker was using since that data got deep-sixed. It's also important to contextualize that, to a lot of people, the twins are still considered Armed & Dangerous. What Wanda is capable of is terrifying. SHIELD doesn't have the benefit of knowing that they are genuinely good people like we do. The only information SHIELD gets out of the Avengers organization is what its members leak to them. That, my friends, I leave in your hands.
I think SHIELD's redemption is rife with potential plot. The organization is operating out of the shadows with good intentions but that is part of the problem. There's no accountability. Keep in mind that I don't watch Agents of Shield (per the FAQ) so I don't reference that material. I see SHIELD as struggling to clean itself up and be the organization that it knows it should be. But it is a struggle because things have been done a certain way for so long. Pietro's resurrection is an example of that struggle. This was a chance to gain valuable information about HYDRA and its access to powerful alien technology that was a threat to the entire world. But SHIELD doesn't have any accountability right now. Reintegrating them with the government could be a step in the process toward fixing that.