We all know if gear was removed from raids, no one would do the raid at all unless it was completely faceroll.
If you must have a raid all decked out in Rakata before attempting EC storymode, then you have effectively removed the gear carrot from the raid. While some raiders will spend some time in there to see the sights and experience the wonders, that quickly wears off when silly mechanics operate in strange ways - like having 3 lightning spires spawn inside the bombardment shields on the tank bosses.
If you have the entire raid decked out in rakata then you should probably start thinking about upping the difficulty a bit and shoot for the higher stuff. If they are still wiping hard on the bosses in story mode EC even after say a months release then I got some bad news for that raid.