Kyiv is and will always be the proper transliterated version of our capital.
I won't address the political statements, as that sort of discussion is off topic for this mailing list.
Now, that said, I'm not entirely sure that it wouldn't be possible for the tz database to consider "Europe/Kyiv" as a name change from "Europe/Kiev" with a compatibility link. Wasn't a similar change made for Asia/Calcutta => Asia/Kolkata ? Or do different rules apply since the name was officially changed by the government in 2001? (http://en.wikipedia.org/wiki/Kolkata#Etymology)