Oh, certainly. But I find it hard to believe that these agencies would keep the support of the public if they started assassinating Congresspeople. At some point there's too much opposition to make it feasible to continue on.

Really, though, I'd expect them to maintain Congress' support through non-lethal means. Bribery, blackmail, stuff like that. A Congressperson in your pocket is much more useful than a suspiciously-dead body.

But still, if US citizens as a whole really wanted them gone, they'd just continue voting in people who will take a hard line against funding them.

I don't expect something like this to come to pass, mind you, but it's possible.