That is not what happened. Congress did not purport to change the rules of federal court procedure, and if they had, the law would never have made it out of the Senate. The Whittemore case acceped de novo jurisdiction, at least for the moment, and then applied the unchanged law and rules to consider an injunction motion. You may not like it, but that was and remains the law. I suspect in time the law would have been deemed unconstitutional, but that was not in play here, and will not be, because the case is now moot.
You make a good point and present an interesting dilemma. Congress clearly directed that the federal courts should hold a de novo hearing without regard to the State Court determinations. There simply is no way to effectuate that direction under these circumstances without granting a stay and ordering the feeding tube back. As the dissent in the 11th Circuit pointed out, the courts could have used the All Writs Act to keep Schiavo alive to have a reasoned hearing and review of the case. Your point about unchanged law and rules regarding injunction motions is valid. However, the judiciary frustrated rather obvious congressional intent when it could have just as easily implemented it. There would have been a lot of value in the airing of the serious constitutional issues and defining the boundaries between the three branches. Now all we are left with are hot rhetorical statements from the courts and a moot statute. I continue to believe that there is a much larger governmental issue here than fine legal arguments and rhetorical flushes. This is simply another in a long line of recent instances where the judiciary has declared itself superior to Congress.
By the way, the basis for the statement that the courts told Congress to pound sand is the intemperate opinion of Judge Birch.