Congress can exempt federal laws from the RFRA. I don’t think it would have a chance of passing, though. The Hobby Lobby decision was mostly about the applicability of the RFRA rather than a constitutional case.
Special legislation to apply something negative is much tougher. If this is what Harry Reid means when he calls for doing something about the Hobby Lobby case, I cannot think of any precedent, though I'm sure there must be something such as some of the stuff Lincoln did during the Civil War.
Under normal circumstances, special legislation to apply something negative would fall in the same general category as a Bill of Attainder or an Ex-Post Facto law and be thrown out.