The StackExchange model is based round the idea that the sites are not forums, but that questions and answers should have some element of generality. As such, 'good' questions should be focussed on the matter in hand, ideally without many things that might make good forum posts. That's one reason that 'thanks' is discouraged and why community edits are allowed.
At the same time, each question does have an original poster (OP) who has some element of 'ownership' (their name is on the question, after all). The usual guideline is that edits shouldn't fundamentally alter what the OP said. Some people are particularly keen on a very specific form of words, style, or similar, and thus may feel that edits to 'standardise' their text are not what they want.
What we have to do is balance these two situations. My take is that editing to remove 'thanks' is reasonable (it's in both the site and cross-network 'spirit'), but that having an editing war to do that is not. So if the OP decides that they really do want the 'thanks' in, it's not a big issue to accept this and move on.
Note that the moderators do have tools that can be used for 'edit wars' and which can prevent any edits at all. In general, we will not use these unless really needed, and I think it's fair to say a case about editing 'thanks' isn't one I'd like to see them used for!