I think Thomas writes things like this just to rub it in the face of all those liberals who opposed him on Anita Hill grounds, rather than just being honest and disagreeing w/ him b/c he's a conservative and doesn't toe the liberal line.
That's it in a nutshell -- to exclude certain choices on Establishment grounds represents an establishment in its own right: "you can use this anywhere except at a religious school."
Did the decision just come down? Vouchers won?!