the Doctor has mentioned on a number of occasions that "time can be re-written" I'm guessing this is what happened once Rory was absorbed by the time energy.I was then alivePeople assume that time is a strict progression of cause to effect but actually from a non-linear, non-subjective view point it's more like a big ball of wibbly wobbly timey wimey stuff... :D
Basically, this is due to the fact that he had not been absorbed at that time so events had not been changed.