Brainiac
Super Freak
Well, Hydra was still flying under the radar within SHIELD -and I got the impression they needed to be until Project Insight was completed. If a lot of high profile/famous SHIELD agents like Fury and Cap were taken out that would could cause scrutiny too early when they weren't ready for it. They got to be as powerful as they became by being snakes in the grass.
I think WS was sent after Cap because Pierce knew they were out of options and Project Insight was too important to them not to risk it - I mean, who else could stand a chance against Cap? They threw a bunch of hardcore dudes at Cap at SHIELD and he rendered everyone of them in the elevator unconscious. Guys like Rumlow didn't stand a chance against Steve, and then there's Widow, who definitely adds to the challenge (speaking of Rumlow, they're gonna have to supe him up in some way in Cap 3 if he returns, otherwise I can't see him lasting long against Cap or Bucky, and Widow would get him, too, I think, though it would be a fairer fight).
I would say Cap became a danger to their plans the moment Fury survived the assassination and sought him out. Surely they knew Fury was talking to cap since TWS killed him when he was in Cap's apartment(unless TWS tracked fury by himself), why not give TWS orders to kill Cap or whoever he was talking to as well. As for assassinating prominent SHIELD members too early your right they needed to stay hidden until the Helicarriers were online, but there is a point where it becomes recklessness and stupidity not to cover your tracks.
IF Rumlow comes back and I'm guessing he will I would imagine they would have to enhance his abilities in order to give him a chance since he obviously wasn't good enough to go toe-to-toe with Cap in this movie