Separatists in Government
I have trouble seeing how there's anything particularly wrong with separatists running for, and attaining, leadership positions in the country they wish to separate from. The idea that it's illegitimate seems to come from thinking of the country as an entity with its own interests -- in which case, it does seem odd to give control of it to someone who opposes its existence.
But countries don't have interests independent of the interests of their members. Governments are tools created by groups of people to implement policies in the interest of the citizens. One such policy may be to rearrange the borders of the country. That may very well be a bad policy -- but there are lots of bad policies a party may wish to implement (from what I saw of the Alaska Independence Party's platform, seceding from the US was about the least objectionable plank to me).
To say that separatism is an inherently illegitimate policy for a governing party to support implies one of two conclusions, neither of which strike me as particularly palatable:
1) Separatism, if it's a good policy, must be pursued outside the normal policymaking process -- which means armed rebellion. I don't think I'm alone in preferring to go the way of Czechoslovakia rather than Yugoslavia.
2) Separatism is an inherently illegitimate policy -- it's wrong to want to alter the existing borders of countries. But how can we say the current borders, most of which are accidents of history, are sacrosanct?
It's fine to oppose separatism for Quebec or Alaska on the merits, and on that basis to oppose politicians who back those policies (I actually don't have a real opinion on those issues). But there's nothing illegitimate about them proposing such policies, or of winning high office while supporting them.
*Ties which turned out to be much less significant than initial reports suggested.