I think it's easy to see the conceptual problem in having two subspecies and then a third undefined member of the same species whose scientific name includes those two subspecies.
But I don't see much problem if the timber wolf is renamed as any subspecies. As it has been said, they are very similar to other cool-climate wolves, so you could still use it like any of them. For example, now that you mention it, I use the Formosan black bear as non-Formosan subspecies too. Or if I want a Kamchatcka brown bear, I use the grizzly bear with no problem. But wouldn't it be weird if the grizzly bear was called just "brown bear" while we have an Himalayan brown bear?
Or for example, if they add the quagga, they should rename the "plains zebra" as "Burchell's zebra" or something like that even though it's clear that our plains zebra is not based on the quagga subspecies.
And let's not forget that in some languages that wolf is translated as "MacKenzie wolf" or something similar referring to the C. l. occidentalis subspecies. So it's only the scientific name what is wrong. Maybe just because "timber wolf" can't be translated, maybe because Frontier based it in that subspecies, probably both.