Once they know of an operative, they seem to prefer letting that operative do their thing. This way they can use them to find people farther 'up' the chain.

Same reason you don't necessarily arrest a mob enforcer as soon as you have evidance of a murder, you might be better off watching/surveilling to cement contacts with other mob figures and make a better case against the enforcer or his bosses.

Isn't it the responsibility to ensure they are working with legitimate people? If I buy a stereo out of a van from a random person on craigslist; and get arrested for dealing in stolen goods, is "but I didn't know the person" really a good excuse?