Willing to bet that Rehnquist has fundamentally changed his mind in the last twenty years, are you?
It doesn't matter. That's where the Supreme Court decision in Landgraf comes into play. Federal civil statutes cannot be applied retroactively without specificity by Congress.
In other words, and especially if this were a criminal matter and not a civil one (ex post facto) - the laws in force at the time of the alleged misconduct are the laws that will apply in court.
Interpretation of the law is guided by legal precedent. The precedent in this case would not favor Rehnquist's view when he dissented in Thomas v. Review Board.
The only thing that can change this legal calculus is if the case at hand is appealed all the way to the Supreme Court and the court overrules itself. And that very, very rarely happens.
This is true, but not relevant to how the Court might rule on such issues in the future. First, the state of the (statute) law regarding the Establishment Clause and the First Amendment is essentially the same now as it was in 1981, when Thomas was decided - the only applicable legislative initiative in this area since Thomas was the Religious Freedom Restoration Act (RFRA), which has already been struck down as unconstitutionally vague in the 1997 case of Boerne v. Flores, and the Religious Land Use Act does not seem applicable.
Interpretation of the law is guided by legal precedent. The precedent in this case would not favor Rehnquist's view when he dissented in Thomas v. Review Board.
Second, this does not implicate Landgraf in any way, shape, or form - the retroactivity requirement explicitly applies to statute law, not case law, else courts would never be able to overrule themselves at all. And it's a rather contentious assertion to begin with - see, e.g., Employment Division of Oregon v. Smith.
The only thing that can change this legal calculus is if the case at hand is appealed all the way to the Supreme Court and the court overrules itself. And that very, very rarely happens.
Essentially, this argument boils down to a tautology, claiming that the Supreme Court cannot overrule itself, unless it...overrules itself. While this is trivially true, as are all tautological statements, it does not illuminate the circumstances of such a decision, or tell us anything we didn't already know. When Rehnquist has clearly telegraphed his disagreement with Thomas in such plain and firm language as in his dissent (and such reasoning has already been adopted by the Court as per Smith), it is not particularly realistic, IMO, to believe that they will set such disagreement aside merely to remain consistent with the precedent set by Thomas.