There's definitely room for more answers that specifically discuss Washington and the Whiskey Rebellion, but there's a section of the /r/AskHistorians FAQ titled Gun Control and Second Amendment Culture In The USA with several answers about the rationale behind the Second Amendment, including this very detailed post by /u/uncovered-history: What was going on in America that caused the Founding Fathers to create the Second Amendment and sign it into law?

Thanks to /u/hillsonghoods for linking back to my answer I gave a few months back. I'll explained a little further because I think there's something I should clarify about your question.

In your question, you assume that the Second Amendment was created specifically to allow citizens to overthrow the United States government. Despite the popularity of this belief in some circles over the last few decades, this is not the case. As outlined in my post, the Second Amendment was created during a period of civil unrest in the United States with multiple accounts of rebellions of agrarian insurrections happening throughout the 1780s and early 1790s. The creators of the US Constitution and Bill of Rights new this and were very troubled by it. The only way they could account for fighting these insurrections, when a standing army practically did not exist and police forces were not yet founded, was to have members of the gentry call up militias to put down rebellions. This happened in several places, most notably in Massachusetts and his Regulators. The founders thus protected an individual's right to own firearms with this mindset. So the reason why Washington put down the Whiskey Rebellion was because this was the precedent already established since the Founders did not want to ousted from the government they were still in the process of establishing.

Now, I want to do some debunking on here, if that is okay. Many people believe, as you pointed out, that the 2A was created so that people can rise up against the government. Again, this is, at best, an exaggeration of the views of a minority of the founders, and at worse, just a flat out lie all together. Why do people think this way? For several reasons. The first, is that there is a growing list of false quotes attributed to many founders that people like to use. Websites run by the museum's of both Mount Vernon and Thomas Jefferson have webpages that actually debunk these quotes. They explain how quotes like ""When government takes away citizens' right to bear arms it becomes citizens' duty to take away government's right to govern," have no origin in any written or verbal documentation on record. And for the record, we have over 32,000 pages of Washington's writing and almost 20,000 pages of Jefferson's writing transcribed and keyword searchable and more that are left in their written form. This link also provides debunked quotes for Jefferson. I'd also like to disclaim that there are many, many fake quotes out there for all the founders, that range from the 2A, to religion, to the purpose of government, on and on. Some of these quotes and stories even date back to the 1800s (Such as Washington chopping down the cherry tree which was created by Mason Weem's in his 5th edition of his biography on the life of Washington, published in 1805).

You’ll also see quotes mismatched and pasted together in order to argue for strong 2A views. A good example of this can be seen with this quote by George Mason. Many 2A websites post this quote:

"To disarm the people...[i]s the most effectual way to enslave them."

However, this cuts and pastes around what he was actually saying. Here’s the whole, unedited quote:

An instance within the memory of some of this house will show us how our militia may be destroyed. Forty years ago, when the resolution of enslaving America was formed in Great Britain, the British Parliament was advised by an artful man, who was governor of Pennsylvania, to disarm the people; that it was the best and most effectual way to enslave them; but that they should not do it openly, but weaken them, and let them sink gradually, by totally disusing and neglecting the militia. This was a most iniquitous project. Why should we not provide against the danger of having our militia, our real and natural strength, destroyed? The general government ought, at the same time, to have some such power. But we need not give them power to abolish our militia. If they neglect to arm them, and prescribe proper discipline, they will be of no use. I am not acquainted with the military profession. I beg to be excused for any errors I may commit with respect to it. But I stand on the general principles of freedom, whereon I dare to meet any one. I wish that, in case the general government should neglect to arm and discipline the militia, there should be an express declaration that the state governments might arm and discipline them. With this single exception, I would agree to this part, as I am conscious the government ought to have the power.

Can you see the difference? He’s exclusively talking about the relationship of arming people for a militia and the role of government in doing so. Now I’m not saying that the same principle can be applied to every real quote out there, but this is far from the only example. This point is clear: the founders protected an American's right to own firearms, but they did not do this so people can overthrow the government.

Please let me know if this makes sense or if you have any follow up questions.