Thru-hiking the AT and becoming a 2,000 miler is very similar to completing peakbagging lists in terms of thie following: in each case if a hiker believes he or she has, to the best of their ability, completed the trail or the mountains on the list, then IMO, they have met the "requirements."
I was a purist on the AT and hiked every white blaze including a section I returned to later on that was on fire during the hike (Shenandoah). I was not "required" to do this since it was on fire - this was a personal decision. Hikers dealing with the aftermath of the storm will have plenty of legitimate reasons to hike alternate routes. I wish them all luck with their trip through NE.
I also however am a firm believer in HYOH. A person can hike the AT any way they want. That's their business. 2,000 miler requirements are quite clear though if one decides to apply for it. There is not much ambiguity in the application.
I would think most of the peakbagging community would have an issue with someone who hiked 43 of the 48 in NH and decided to apply for the 4,000 footer club anyway because they opted to do 5 different mountains instead.
Regarding the Kennebec, I would imagine Steve Longley (or his replacement) has a white blaze on his canoe at this point.
Everyone associated with the AT has an opinion on this. The point of the hike is really not the certificate and patch anyway, right?