The most glaringly obvious difference between the two cases is that the Kosovo secession occurred in the aftermath of the genocidal mass murder of Kosovar Albanians by the Serbian government in 1998-99. By contrast, there is zero evidence indicating that Crimea’s majority-Russian population was threatened with any remotely comparable atrocities at the hands of the Ukrainian government. Indeed, the most recent genocidal mass murder in modern Crimean history – the mass deportation and partial extermination of the Crimean Tatars – was committed by the Soviet Union, the regime to which Russia is the successor state. Today’s post-Soviet Russian government is not responsible for that atrocity. However, it is worth noting that Vladimir Putin is a former high-ranking officer of the KGB, the Soviet government agency (then known as the NKVD) that played a major role in the Crimean genocide and many other Soviet atrocities, and that Putin is today a leading apologist for the USSR, whose collapse he called “the greatest geopolitical catastrophe of the twentieth century.” So long as the likes of Putin hold power in the Kremlin, Crimea’s Tatar minority (who are a minority only because the Soviet Union previously exterminated and deported nearly all of them, before allowing some to move back in the 1980s and 90s) have good reason to oppose the return of Russian rule to Crimea.
A second crucial distinction is that the independent government of Kosovo, while far from perfect, adheres to liberal principles and respects human rights at least as much as newly democratized Serbia does. Therefore, Kosovar independence did not lead to any significant oppression that would not have existed otherwise. By contrast, as I discussed in this post, Putin-era Russia, while less oppressive than the USSR, is guilty of numerous human rights violations and is likely to engage in similar practices in Crimea.
Finally, while there is little if any doubt that the vast majority of Kosovo residents supported independence in 2008, the recent Crimean referendum on independence was likely tainted by fraud and intimidation. Polls conducted before Russian military forces occupied the peninsula indicated that only a minority of the population supported reunification with Russia. At the very least, the 97% pro-annexation margin in the official tally for the referendum was utterly implausible. Majority popular support is not necessarily sufficient to justify secession. But to the extent that its presence or absence is morally relevant, it was far more clear in the Kosovo case than in Crimea.
Finally, it’s worth noting that the Russian government vehemently opposed Kosovo’s secession, claiming that it was illegal and unjust. If we take Russia’s position seriously, then secession cannot be justified even in the aftermath of mass murder. By that logic, it is even less defensible in the very different circumstances of Crimea today.
Far from justifying Russian policy in Crimea, the comparison with Kosovo further underscores its indefensible nature.