Note that what we’re talking about here is secession, not a civil war.
Secession is moral under certain circumstances. One, with the consent of the larger polity. If Czechoslovakia consents to the secession of Slovakia, then there’s no problem. But there are all sorts of details to work out. What happens to people who live in the seceding territory, but want to remain citizens of the other territory? What happens to national debts and national assets and national obligations?
Or, if the larger polity is oppressive, then the smaller units can morally secede. This is the justification for American independence from Britain. This is a subset of the inherent right to resist oppressive government by force. If you live under tyranny, you’d be morally justified in fighting back, even if only to win freedom for a portion of the territory under tyranny.