Reading the Doc's article on the last LOST episode and the theroies presented on time travel and what the death of Ben's Daughter means:

 "My interpretation of ''He changed the rules'' wasn't so much Widmore and I agreed to wage our battle according to a certain set of limitations and regulations, but rather, simply This was not supposed to happen. As I've long insisted, I believe Ben's genius is derived from having knowledge of future events, via time travel, Desmond-esque precognitive flashes, or the other hot conjecture of the moment, time-loop theory, the idea that Ben has lived this life many times before. So a monkey wrench like this pretty much wrecks Ben's entire game.

 My challenge with this thought process is taken directly from one of The Doc's own interviews with some of LOST'S creators:

http://www.ew.com/ew/article/0,,20179125,00.html

DOC JENSEN: Another popular theory making the rounds is that we're dealing with alternate realities. For example, there are people who think the flash-forwards are merely possible future scenarios, not written in stone.

CARLTON CUSE: We want people to believe in the stakes of the show. The problem with alternative realities is that you never know when the rug is going to be pulled out from under you. We want the audience to believe that the jeopardy is real. Postulating alternative realities would be an escape valve that would be damaging that as a narrative value.

DAMON LINDELOF: We're not going to tell you that we're against bending the time-space continuum. We are very for it. Carlton and I are PRO time-space continuum bending! But we're ANTI-paradox. Paradox creates issues. In Heroes, Masi Oka's character travels back from the future to say, ''You must prevent New York from being destroyed.'' But if they prevent New York from being destroyed, Masi Oka can never travel back from the future to warn you, because Future Hiro no longer exists. Right? So when we start having those conversations at Lost, we go, ''This show is already confusing enough as it is.'' To actually have characters traveling through time has to be handled very deftly.

I read this as basically shooting Doc's theories about what Ben said out of the water. It lends itself to the "we are having our own semi-private war" theory once again as it makes the most sense.

I don't have a bunch of awesome and original theories to counteract with. I just know that the Doc's thought process seems off, at least about this anyway.