If you take away the maneuverability of the larger ships you doom them to constant death when they fight smaller ships. Back in Beta 1 they were far less maneuverable, as a result it was very difficult to fight one on one with smaller ships. In group fights where their are always distant targets not paying attention to you yes they are deadly. Until we have crew/player served turreted weapons these ships need their maneuverability to be viable in combat. I have seem eagles take out Elite Anaconda's in game as it is now.
I don't think Anacondas are made for one-on-one fights with, well, fighters. Still, I'm pretty sure that turrets are too weak right now. I don't have very much first-hand experience with them, but it always seems like it's the gimballed weapons that are the biggest threat when I fight larger ships (if they can bring them to bear).
I've seen a Sidewinder take out an Elite Anaconda. That has more to do with the AI than anything else.