A few things to consider...
1. As has been said, THF includes the benefit of damaging multiple foes simultaneously so comparing to a single target can be somewhat misleading.
2. This assumes that you hit on a 2+. While in current end game that is not a terrible assumption, we don't know how valid that will be in 20+ elite content. The Kensai will have a much higher to-hit bonus. It doesnt take much for them to suddenly leap back into contention. If the mobs dont have decent AC though, then this becomes moot.
3. Passive, non-passable, mob DR has a very large effect on this. If we see mobs with 5/- or 10/- DR commonly that the transmuting won't bypass, that tilts things substantially more toward the THF.
4. As has been said, this should really be a Greataxe vs Kopesh analysis. Greatsword has its only failings aside from the TWF vs THF issues or Fighter vs Ranger issues.
Not suggesting the ultimate conclusion is incorrect, just pointing out that the devs have visibility to the above more than we do right now, and hopefully are taking them into account which explains the current disparity. Insert cynical comment here...