Maybe...I definitely get your point. If, however, you stop the plot in question right there at first signs, there is the very real possibility that you stop it before you have sufficient evidence of an actual crime. Then the government's intervention is turned into a violation of civil rights and there is no prosecution or rehabilitation or punishment.
It's a very fine line, and I get the uncomfortableness with undercover government operations in general. I also get that the FBI doesn't have the best track record regarding civil rights, engaging in criminal conduct themselves towards individuals, and honoring that fine line and not way overstepping it.