Some good historical analysis here, but I’m not so sure about the conclusion. I certainly support a right for regions to secede, but not all EU member states recognise such a right. Spain is the obvious example, since while it gives a high degree of autonomy to regions, including enhanced autonomy for Catalonia and the Basque country, it does not recognise any right to secede except through a law passed by the Cortes (parliament of Spain), which is extremely adverse to allowing any procedure for secession.
Greece has been extremely adverse to secession by Kosovo from Serbia, and does not recognise Kosovo, on the basis that a majority vote within a region-aspirant nation is not enough to justify secession under international law, if opposed by the nation from which the secession is taking place. I suspect there are some other countries with similar barriers to secession.
They’d do well to recognise that right, but the EU can’t force this kind of change on existing member states since unanimous consent would be required for the necessary treaty changes, and even without that barrier, the idea of the EU forcing countries to accept a right to secede and then define when and how that right to secede, which could create conflict with counties like the UK which do recognise the possibility of secession by referendum within the relevant region-aspirant nation, as in the current Scottish vote.
The time might come in the future when all EU countries might recognise a right to secede and then recognising that right could be a requirement for membership. However, it is not Putin’s Russia that would be concerned. Recent events in Ukraine show Putin’s agents fomenting violent secessionism in Crimea etc and a rigged referendum in Crimea. Of course Putin’s meddling is not the same a secessionism exercised peacefully and through fair voting, but such differences are likely to be overlooked by many in light of the still unfinished Ukraine crisis.