Then I would agree with you. Why protect him for just a year?
Eh, there are a lot of moving parts, a lot of potential reasons.
a) Perhaps JBB decided we couldn't afford either one -- Gourde or McD -- after this year, and perhaps McD had signaled willingness to waive his NTC and Gourde had not. The expansion draft overrode an NTC (but not NMC, as you pointed out), so that would then be the only way to move Gourde.
b) Perhaps JBB decided we couldn't afford either one, but the issue wasn't NTC's it was the value we'd get back. Maybe Seattle wasn't willing to give us anything to expose McD, and JBB thought we could get more for him on the open market than we could for Gourde when we had to make a move after this season. (If that's the case, I'm thinking he miscalculated.
c) Maybe JBB was thinking we'd keep McD through the rest of his contract and lose other guys instead, but has now decided McD's play has fallen off in a way he hadn't expected, and he changed course.
d) Maybe JBB was looking purely short-term at the threepeat, and felt like keeping McD and replace Gourde with a cheap forward (say, Bellemare) made us a better team this year than one where we keep Gourde and replace McD with a cheap D (say, Luke Schenn or equivalent quality).
e) [many other possibilities...]
In truth, the two big reasons I thought we should unprotect McD was that I thought Seattle would make it worth our while and I thought McD would hang tight to his NTC (meaning the draft was nearly our only chance to get clear of his contract before it went bad). I was wrong on the latter, and I wouldn't be surprised if was wrong on the former.
I do wonder why McD waived the NTC. Was McD just into moving on, or did JBB have to bring up the possibility of waivers, leaving McD zero control over where he ended up?