Except the limitations that FISA imposes do not conflict with the Constitution. Congress is given express power to make rules for the government.
If the objection is that they "unduly" encroach on executive power, that's the primary reason why the President was given veto power. That's the tool that was intended for restraining congressional encroachments.
Things get real interesting around the "ultimate reaches" of power. The War Powers Resolution of 1973 was vetoed by Nixon, but put into law by a Congressional supermajority. The Constitutionality of that law has not been put to the test, but at least Dick Cheney (and many others) hold that it represents an unconstitutional encroachment by Congress. So far the encroachment has been tolerable, but that doesn't mean it will always be followed by a President.
The question of whether or not FISA provides an unconstitutional exercise of legislative power over presidential power is likewise not amenable to a "neat" solution. If the President persists in action that Congress finds objectionable, the House has the power of impeachment. This is a political power at its core, with ultimate exercise by "we the people" at the voting booth.