The twentieth century's greatest philosopher of freedom and reason, Sir Karl Popper, regarded the ‘alleged right of nations to self-determination’ as a catastrophic error. In one of his last speeches, in Prague in 1994, he said
I think that all lovers of peace and a civilized life should work to enlighten the world about the impracticability and inhumanity of that famous – or shall I say notorious? – Principle of National Self-Determination, which now has degenerated into that ultimate horror, ethnic terrorism.
We must fight against such horrors.
It does not follow from this that all secessionist (or unionist) movements are immoral. It is just that the issue of how territory should be divided up into states must never be decided on the basis of the ‘rights’ of nations (or states, or races, or religions…), whether to self-determination or anything else, nor in terms of an alleged right of individuals to be ruled by members of ‘their own’ group. Claims to sovereignty must be independently justified, and for all the usual conservative reasons, the burden of justification falls on whoever wants to change the status quo. And the only legitimate consideration is:
What do the claimants intend to do with the sovereignty, once they have it?
Thus, if a faction wants sovereignty because they would repeal bad laws and pass good ones, and the existing political tradition is incapable of doing that, then their claim is, prima facie, justified.
But if they want sovereignty because they don't like the colour of the people currently in the government, then they have no case. If they want sovereignty because it would give them a monopoly on the revenue from a certain canal, or certain natural resources, then again, they have no case. If they want to repeal good laws and pass bad ones, then they certainly have no case. It may sometimes be best to let them make their own mistakes – which always means, in practice, tyrannising those among them who are not party to the mistake – but that is not because they have a right to do so.
Furthermore, even an entirely justified secessionist or unionist movement is not entitled to use violence unless their reason for wanting sovereignty is that it is the only way to protect the lives or other rights of the people they represent. Violence is legitimate only in defence of human rights. Political independence is not a human right, and therefore cannot justify violence.