Rather simple way to nerf both frames and turtles would be to choose to not use them or define rules for the server on how players should/shouldn't use them. As neither of those are directly connected to GT in a way IC2 is I don't really see the need for changing those things. Also, from what I've gathered at least frame machines aren't really all that cheap nor too trivial to set up well. At least nowhere near as simple as e.g quarry.
Back in 1.2.5 days I had EE2 installed and it was not hard to only use the "stick of mineral probing" from the mod and nothing else.