The rationale (and the one Ron Paul used to vote for the ban when faced with the same quandry) is that the Supreme Court wrongly federalized the issue of abortion when it decided Roe v. Wade. Therefore, Congress has the right to legislate abortion law and pass laws and initiate legal action to lessen the scope and effect of Roe, only so long as that decision exists.
Actually, the 14th Amendment covers Congressional authority in this manner, but doesn’t allow the Court to legalize abortion.