Ahh. you've fallen under the spell. The Whiskey Rebellion was indeed a rebellion. The South didn't rebel. State Conventions are not rebellious factions. They're constitutional ones. The Southern States held conventions, in which They the People chose to alter or abolish their government.
The members of the Whiskey Rebellion had meeting too. Lots of them. They elected leaders and voted to rebel. And they actually had a much stronger set of grievances than the South did. The Federal government really was hurting them --- badly. But they were a small minority and the majority would not listen to their arguments or ease their plight, so by that standard they were morally justified --- as was Washington legally justified if he had hung them as rebels.
Sometimes life's a bitch.