I doubt there's any organization completely free of rats, but let's be honest, an organization that deals in secrets and intelligence is probably going to allow rats to hide a bit more easily.
The first time we tried to deal with rats, I ended up in a safehouse spending a lot of time with Director Fury. I don't know if I really got SHIELD before that, I mean, I knew we helped people, they gave us the whole spill when we joined up, but Ni Fury -- lived and breathed SHIELD. That time taught me more about SHIELD, its history, its goals, than anything they gave me during agent's training -- maybe because I was stuck side by side with people who had dedicated their lives completely to that.
I suspect that even they might ask where the lines were at times -- when you had Pierce at the top who was HYDRA, it's kind of to be expected that good agents might have ended up unknowingly working for HYDRA's ends. I guess I still believe in SHIELD, at least I believe in what it was founded on, what the people I knew stood for because I believe that principle of protection and believing people were worth it was a sound one. Now that SHIELD is gone, I'm still not certain how to focus my energy exactly, but I think I'll figure it out.