In natural languages, established use is what defines rules, more or less. This particular one is not very consistent, I agree. Nevertheless, "na" is normative for a bunch of country names.

Personally, I use "v Ukraine", if only because it's a middle finger to the Kremlin. But I also don't think that the use of "na" necessarily denotes disrespect, or that people should be told how to properly speak their language.

I guess the nearest abstract equivalent to this would be the debate over gender-neutral pronouns like "xe" in English. You have one side laying arguments (many of them pretty good) as to why having such a thing is a good idea; and the other side pointing out that it just feels awkward and non-English-like.