I don't think the President's constitutional obligation to defend the country should be checked or balanced.
Some might even argue that the very existence of a FISA court is unconstitutional, as it usurps the executive's authorities as commander in chief and foreign policy or international relations. The constitution never delegated any authority to the judiciary to decide matters of war and foreign policy, yet that's exactly what the FISA court does.
Anyway, the point you raise is a tough one. If terrorists are to be surveilled (and attacked, imprisoned, etc) somebody somewhere has to identify who the terrorists are. Who should hold that responsibility?
I gather from your remarks that you believe that it should be a judge. Someone who is unelected and serves a life term, unaccountable to the citizenry. A natural choice, I suppose, given that judges are responsibile for deciding important civil matters. But international terrorism isn't a civil matter, is it?
I argue that the constitution names the executive branch as the one that holds this responsibility. International terrorism (Al Qeada, Hezbollah, and the like - as opposed to domestic terror groups) fall squarely under the catagory of national defense and/or foreign policy. The President is expressly tasked with handling these matters, not some judge somehwere.
And as for checks and balances, what stands to check/balance the actions of the men sitting on the FISA court? The man in the white house is accountable to the electorate. The men on the FISA court are (to my knowledge) completely untouchable.