I don't see that as the same degree of incursion into the executive, as "the wall" (a creation of the executive to begin with, adopted by the court) was.
The court is attempting to protect its independence by not bootstrapping a search of unknown "pedigree" and "constitutionality" into a FISA warrant. If that sort of process is adopted, the government could conduct any search it wanted, without a warrant (not saying it is, BTW), then when it learns of any criminal intent thereby, could get a court to issue a warrant. From whence came the probable cause? Never mind that.
Given the small number of likely cases, I think the administration can afford to have the NSA terrorist surveillance cases handled one-by-one as they come up in court. There is a risk however, that the courts would post-facto invalidate the evidence or share it with the accused. I believe that that risk is what motivates Congress, the Courts and the administration to work together NOW, to insure that use of the information in the future is effective against the threat.
I agree the intrusion is not as great, but I still think the court is wrong. If the President is within his constitutional and statutory authority in ordring the NSA surveillance, and he is, then the fruits of that surveillance are lawfully obtained and there is no valid reason to reject it as the foundation for a FISA warrant application. The only justification wold be the wall, which, as aforesaid, has been abolished. The US persons in question receive all the process that is due via the mechanism of the FISA warrant procedures. It's just too bad for them they got caught up in a foreign intelligence surveillance operation. It sucks to be a terrorist. Not saying you could prove a criminal case with the surveillance take, only that it ought to be admissible in the FISA warrant application process.
The FISA Court has demonstrated a repeated tendency to be too big for its britches. Reimposing the wall by judicial fiat after it was abolished by the Patriot Act is, in my view, reckless, obdurate and scandalous in the extreme.