So I don't really think this is as justified as it seems.

Al Qaeda was a non-state actor operating within Afghanistan. There was no real good framework for the US to deal with this. If Afghanistan had attacked us then of course we would invade them and be justified in that but that isn't what happened. We basically invaded Afghanistan because they wouldn't do enough to stop an internal organization from threatening us.

I think this sort of compares to the US, Mexico and the drug war right now. Clearly the drug war has greatly destabilized Mexico and the US, as the main buyer of Mexican drugs as well as supplier of guns to the Mexican cartels plays a major part in this. I think it is arguable that the US could do more to stop this but domestic issues stop this. So do you think that the Mexico would be justified in invading the US in order to put a stop to the supply chains?

Again the problem here is that it isn't really clear how much a state should do to prevent violence from leaving it to entering another state. Afghanistan was an extreme example of this, but like I argued above, there are lesser examples which are less clear.