I think a couple of things must be considered. First, who owns the boat, and why?
If the boat was bought by someone intending to use it, then generally anything necessary to make it useful is acceptable. If bought by a museum, why did the museum buy it -- to preserve an item that is unique because it is the only one of a kind, or because its history was special, or to display as an exemplar of an old boat, or to restore in order to practice/teach restoration techniques, or ??
But there is a prior question that ought to be asked -- is this boat suitable for being used, or is it too rare, too unusual, too historical, too ?? (you name the attribute) to be thrown in the water and paddled away, no matter who the owner is?
To answer that question, I think you have to consider what the item is --
1. one-of-kind (or very nearly one-of-a kind) objects in original condition (even if seriously dilapidated)
2. one-of-kind (or very nearly one-of-a kind) objects in non-original condition, that is, on which repair, renovation, or other post-creation work has been done in the ordinary course of using the item
Note: an item might be unique because, even though it is a common item, is has a special history -- an ordinary birch bark canoe owned by FDR, for example.
3. rare, but not unique or nearly unique, items in original (or near original) condition
4. relatively common old items in original condition
5. relatively common old items in "used" condition
6. everything else, that is, commonly available items, new or old, in whatever condition.
Class one items should usually not be subject to ordinary use and the wear and tear accompanying ordinary use. Sometimes, though not always, they should be kept as is, except perhaps for very careful cleaning by someone with curatorial conservation training. However, even with such items, sometimes keeping things as is can actually be destructive, and intervention is necessary to preserve the object, even if it means introducing new materials or removing original. Preserving a building often means new paint, replacement of rotten sills and other wood, repointing masonry, and even replacing spalling bricks and stones. Preserving a painting may mean, in addition to cleaning, the removal of an original coat of varnish, or the relining of the painting, or after repairing a rip, cut, or other damage, adding paint to conceal the damage. If an item was flawed to begin with (Wright's Falling Water is a building that comes to mind), substantial new work and material never envisioned by the original builder/artist may be needed (unless the point of keeping the item is to educate and to demonstrate how bad design or execution may lead to failure). Class two items should probably be treated much the same as class one items.
Hopefully, any WCHA member having a very rare boat in these categories would recognize it and treat it accordingly.
The owner of items in class five and six should feel free to use the item as is, or repair or restore it in any way desired. I have a number of Stanley Bed Rock planes on which I have cleaned all the unjapanned metal, flatten the soles, ground and honed the blades, repaired and reinforced cracked totes, refinished the scratched and blistered paint and varnish on both wood and metal parts, and generally converted them from well-worn and/or damaged pieces of near junk into useful, attractive tools. These were not museum pieces to begin with, and leaving them in as-bought condition would have served no purpose whatsoever. While not common, there are plenty of Bed Rocks around, almost none of which are of museum quality. Most of the canoes that are seen on eBay or are discussed in the forums fall into these categories.
But the treatment of items in classes three and four is more problematic. A museum should have a policy, determined by its mission, on how to handle such items. Most, I would think, should probably have preservation strongly in mind in determining what to do with such an item. But I think a private person should feel free to take most any course of action with an item of this sort -- and if stripping and refinishing a relatively rare canoe makes other, similar but non-refinished canoes rarer and more valuable, so be it. I think it acceptable for a private person to chose present actual use, utility, and beauty rather than setting something aside in hopes of a possible future increase in value. This seems to be a zero sum situation -- the "loss" in value by using or restoring such a boat now is offset by the increase in value of some other untouched boat.
The eBay canoe that is the subject of this discussion appears to be rare, but not unique, in that it seems to have its original finish and canvas. From the evidence available on eBay, the purchaser is someone who fishes (and also collects antlers, has an interest in archery, and in Navaho Rugs). If he plans to use the canoe for fishing, he probably should re-canvas and revarnish the canoe -- not just for looks or for better performance, but for the protection of the boat itself. An old canvas cover with cracked paint and filler will likely leak, and the worn and weathered varnish will provide little protection from water and UV damage to the wood. But if he's just going to hang it in his hunting lodge, his sporting goods store, his restaurant, or his bar, it would be easier, and maybe just as well, to leave it as is.
But if the buyer is not going to display the boat, there is no reason in my mind why the boat should not be put into whatever condition that will serve the owner's purpose and sensibility.
The reality is that in our individualistic society, an owner can do pretty much what he wants -- hence canoe bookcases made from Peterboroughs and coffee tables made from Rushtons -- and the ignorant and insensitive will do unfortunate things unless and until they can be educated. The blockheads will do unfortunate things no matter what. All we can hope for is that we ourselves will try to be aware that there are issues to be considered, keep from being blockheads ourselves, and maybe along the way educate others about the values we see in wooden canoes.