Yes, this usually means exactly that. For example, that Crimean Tartar community members were kidnapped, arrested, disappeared, deported or killed before, during and after the referendum. It also means that vote counting was rigged, ballot stuffing was prevalent, people were coerced into voting, and that the very question posed in the referendum was completely biased.
> Here they try to imply that the objective is to kill every Ukrainian while not explicitly mentioning it, while it seems that the goal is to instead eliminate the idea of Ukrainian separatism. (kinda like Spain and Catalonia)
Your statement seems to imply that Ukraine is not a sovereign country, otherwise it pains me to understand how it could be 'separatist'. Care to elaborate?
Russia's official statements regarding Ukrainian sovereignty, nationhood, and nationality do speak of 'elimination'. Russian actions in occupied territories of Ukraine indicate that this is, indeed, one of their war aims. Since the elimination of a nationality and its culture is what's known as committing a genocide, I have to ask: are you saying that Spain is committing a genocide in Catalonia?