In the beginning yes, there would have had to be incest. However given a clear effort over a relatively short time the population would grow so large that it wouldn't any longer be detrimental to the gene pool and natural selection could start to weed off the ones that were unfit, leading to the mostly genetically A-OK humans we have today.
For example, assuming Adam and Eve had plenty of children (Like 10 children) and then each pair (5 pairs) had another 10 kids
(eugh), there's now 50 new people. Then 250. Then 1,250. Then 6,250. You get the picture.
So no, that's not a valid argument against Christianity. (There are of course other ones for this particular flavour of creation story that I won't get into.)
Anyways, defending the belief side, I think there might have been design choices to prevent incest from being a problem in early generations
If you have only two people on earth, and they have babies, in order to make new babies those children would either have to either procreate with their parents or eachother. The fact that there was incest is an unfortunately unsolvable fact. It's gross as hell but it wouldn't cause an early end to the human race.