That's the big, big problem!
Let me give you a few well-known countries and you can think about whether there are any parallels between them and Afghanistan.
1 England: the English Civil War (very simplified description). The terrorists as we would call them nowadays [the Parliamentarians] won and King Charles I was executed. The people that now rule the UK have inherited the system of government originally set up by those victors. (Yes, there have been changes but we've stopped executing kings).
If we had Dr Who's Tardis and took a modern army back to restore the monarchy (the then rightful heir to the throne King Charles), then would this be a legitimate exercise?
2. What about that rebel mob of colonies in the US led by Washington in 1776? They defied the rightful King of Great Britain an Ireland, George III, and many, many people on both sides died during their act of succession.
3. Then there's the American Civil War/The War Between the States. It can be argued strongly that Lincoln started the war; and or did nothing to stop it or defuse the tense situation between the time of his victory in the polls and that of his inauguration.
In the process of saving the Union Lincoln started a war that killed more Americans than in all other wars that the US has fought in ever since - Spanish, WWI, WWII, Vietnam, etc. Like Pontus Pilate, he sat on his hands and did nothing to stop it.
It can be argued that by 1860 slavery was on the decline world wide and that given several more decades the South would have been forced to abandon slavery due to pressure, sanctions, from other countries such as the UK. A trade embargo on Southern cotton would have bitten the South very hard.
In the grand scheme off things, Lincoln could now be classed as a war criminal for starting a war that killed somewhere between 600,000 and a million people. Do the utilitarian equation - was that number of lives worth it when waiting a decade or two may have seen the same outcome? When you consider the inequlity and illtreatment that negros have had in the intervening 150+ years since the War then the answer may not be so obvious.
Today, current rulers in Washington are the beneficiaries of both of those conflicts. Thus one could ask the question about how legitimate is their rule nowadays (many Southerners would still probably question the victor's legitimacy).
4. 1789 France. The French Revolution culminated in the execution of the legitimate king of France Louis XVI in the Place de la Concorde by mob of essentially out of control 'terrorists'.
What followed was The Reign of Terror (la Terreur) - barbarism, death and destruction beyond anything seen since the Crusades of the 12th and 13th Centuries and not equalled again until the Nazis came to power in the 1930s.
The current government of France has inherited many aspects of that violent revolution and now claims legitimacy to rule the country as a republic instead of a kingdom.
5. The same goes for the Russian Revolution of 1917 and the murder of the legitimate czar of Russia, Czar Nicolas.
I hear everyone saying hey, hey now. However, think about it for a moment, most of our governments today have their historical routes in one form of insurgency or revolution or another. Governing the world is no easy matter and it's always been thus.
I'm not here to argue one way or other except to say you're correct about Afghanistan but then that's only correct inasmuch as to who one considers to have legitimacy. My view is that the poor longsuffering ordinary people of Afghanistan should be allowed to live and run their lives as they see fit without hindrance and interference. But then that's taking the naïve view and it's certainly not the current reality.
Yes, terrorism is alive and well
Afghanistan but it was also the case in Vietnam with the Vietcong. Now, that's all over and friendship has been restored between the belligerents. Trouble is that two million people had to die in the process.
Afghanistan has had a rotten time for much of its existence, especially so since the British tried to tame the country in the 19th Century.
Many of the troubles in the Middle East in the 20th Century can be traced back to the dissolution and break up of the Ottoman Empire after WWI together with interference from Western countries, the UK, France etc. Problems that arose from those ill-considered policies which were forced on those countries more than a centuary ago are still with us today. For example, the 1917 Balfour Agreement was a well meaning but somewhat failed attempt to sort out the Jewish-Arab problem in that area of the world and it is still in an unmitigated mess today.
Whenever grand political policies are introduced always expect there'll be fallout from them for hundreds of years to come.