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.
We actually started directly in HM EC just to see what it was like. Overall, I thought we did fairly well. On our 3rd attempt, we had Toth/Zorn down to 74% or so. Our second raid night, we decided to just go ahead and knock out our story mode quest - since we didn't believe we'd get credit for doing it in HM.
To me, minus a mechanic or two - it didn't really feel that much different. We killed Toth/Zorn but it certainly didn't feel like the step down that I was expecting from hard mode to story mode. As it is, I expect only a handful of raiders to complete storymode EC as it is right now.
Again, if you must have gear only acquired from hardmode EV/KP - then storymode EC seems out of place. I imagine there will be some nerfs to storymode.