Making Desmond an exception of any sort has the same problem. I also would dislike lame "reasons" like surviving the destruction of the hatch. The storyline about the numbers preventing the end of the world has been detonated already. It was a dud. Revisiting it would just compound the error.
Well yes, it makes no sense if Desmond is an "exception" in the sense that he can create alternate timelines. The writers can't have it both ways. Either there's only one timeline or there isn't.
But there's no logical contradiction if, as I suggested earlier, Desmond is only "special" in the sense that his memory is swiss cheesed. In that case, there isn't necessarily a problem. It would mean that, for example, Desmond's meeting with Faraday at the Hatch was always part of the timeline, but Desmond simply forgot about it because his memory's messed up, and then remembered at a convenient time years later.
That would mean that Desmond represents a highly convenient escape clause for the writers, but it wouldn't violate the laws of physics.