Isn't their government currently illegitimate because they refused to hold elections?

Fact is, if Russia wanted to overthrow Zelensky they would've done it by now. The problem isn't Zelensky, but the entire notion of Ukrainian independence from Russia. Until Russia can comprehensively beat that idea out of the Ukrainian ethos, this war will not end.

See also: US-Cuba, China-Taiwan, and historically US-South America under the Monroe Doctrine.

Note that this idea isn't about domestic sovereignty insomuch as it is about who your allies can be. If Ukraine were independent but in CSTO or even in BRICS, there would be no issues. Similarly, if Cuba were to be a US ally instead, sanctions would be dropped and it would be welcomed with open arms.