Yeah, but the people who joined it thought they were using their weapons against a tyrannical government. Fortunately for everyone involved they left rather than challenge a serious army, which made it politically possible to pardon them (if they killed soldiers I doubt the survivors would have gotten off so lightly). The law got repealed because Jefferson didn't like it from the beginning, not that the Whiskey Rebellion changed anyone's minds.
Presidents don't repeal laws by themselves. There was enough irritation over the law, made extremely public by open, if short lived, rebellion, that heads rolled, politically. The tax itself adversely affected a small minority of the population, would the majority have cared enough to get it repealed otherwise?
And which side do you think is the majority and minority here? Surely you're not saying its a good thing we had to fight the bloodiest war in our entire history to settle two political questions, no matter how important they were.
The minority was the south. Slaves weren't really people to them, so there weren't anywhere near as many southerners as there were northerners. 
Without the civil war, how long would slavery have dragged on?
If the south had seceded, the US wouldn't have become a global power. WWII would have gone very differently, with a wonderful chap by the name of Stalin holding sway over most of Europe, maybe all of it. The UK would have fallen to Germany most likely, if a short lived defeat. It would have been a rather dark last several decades I expect. It wouldn't be unreasonable to assume that most of the western world would be totalitarian dictatorships instead of democratic nations.
If they hadn't seceded and kept dragging along within the union as is, they'd have been slowly crushed. How long though before it came to a close, another generation, maybe more? They could never have gotten that amendment through the full congress at the time. How long before additional states were added to the union to tip the scales?
Ignoring the morality, it was still a terrible thing to let continue. Slavery was more stupid than evil. That's not to say slavery was wonderful, just that it was an amazingly stupid way of doing things. Economic productivity exploded in the agricultural sector, after slavery ended. People stopped doing things with sheer manpower and started thinking about doing it smarter. The south might have destroyed itself by the time slavery ended peacefully. They'd already depleted the soil so severely that the only thing you could make a living growing on much of it was peanuts.
Some times people have to kill each other to get shit done. The French needed their revolution to get out from under the aristocracy that had abused them for generations. The rest of Europe needed to see the French murdering entire families in the wave of insanity that followed. It finished the feudal system, and nothing short of slaughter was going to accomplish it before the civilizations collapsed. People aren't rational. It can take a great deal to break through the barrier of sheer stupidity that we convince ourselves of.
This thread is a glowing example of that. The second amendment is plainly written with the reason spelled out, and we've still got most of the country believing the lie they tell themselves. The founders meant for the people to be able to match and kick the crap out of the government that served them, yet we're reduced to arguing over how much you really need to defend yourself in a robbery.
