This question has puzzled many people. Regarded as incest today (and also in the Bible!), it seems to have been ok early in Scripture. As a matter of fact, some skeptics have regarded incest as a contradictory issue, since Abraham, Isaac and Jacob all married relatives and later in Leviticus 18:6-18, it is clearly prohibited.
I agree with Norm Geisler and Tom Howe in their view of incest. At the beginning of the creation, Adam and Eve were created without genetic imperfections. The result, then, of apparent incestuous relationships between Abraham and Sarah, Isaac and Rebekah and Jacob and Rachel, was no condemnation from God. The prohibition came once many generations had passed and sexual relations between family members produced offspring that were adversely affected as a result of it.
I am convinced that the Bible’s apparent contradictions can be resolved with deeper study, or will be resolved eventually through archeological discovery. God’s Word is trustworthy.