I don't think they can get rid of the timer until they've cleared up some server related crap (or added more servers). I've yet to take part in one of the raids, but I do remember some talk of a limited (not sure how limited) amount of instances that can happen at once. The timer is just to keep players from hanging out in the instance too long at the moment. I'm sure at some point in time it'll be done away with along with the minimum player requirement. But probably not until they can handle an abundance of instances at one time.
And on a side note... Do the cut-scenes require you to hit a button to progress the dialogue? If so, that's why the timer keeps ticking down.