The obvious resolution to that paradox is either you don't understand Chomsky's morals or have mistaken what his beliefs are.
Judging by some random interview from 2022 [0] it looks like he has a position on Russia/Ukraine that is easy to defend. He describes it as a "principled, internationalist, anti-imperialist left response" and that seems like a fair assessment from what I'm reading. Looks like pretty standard fare for anyone who doesn't like war and propaganda.
https://chomsky.info/20220204/
Oh also his georgian take https://chomsky.info/200809__2/
He has made some good points about western politics from time to time. Even a stopped clock is correct twice a day.
NATO continued to expand right up to Russia's doorstep despite repeated promises not to, and refused to rule out expanding to Ukraine. Russia clearly called this out as a problem for years. Whether or not this is "NATOs fault", it's clear that the Ukraine invasion was motivated, in part, by NATO expansion.
NATO is an aggressive alliance that has exclusively invaded three countries in the last 20 years, zero of whom were threat to it.
The worst one was probably Libya, because NATO pretended to engage in a humanitarian mission to gain approval from the security council and then left the country utterly destroyed state afterwards. The country was shredded.
It's a tool of western imperialism that dangles the false promise of protection. In this respect it operates with the same logic as a gang recruiting teenagers before using them as cannon fodder.
Of course you can't say these things in polite company just as I couldn't say that WMDs were a complete load of bullshit in 2003 without being verbally attacked.
In 20 years time it will be seen as obvious, however.
Which other countries did NATO invade?
No country was forced to join NATO. In fact, it took years and years of lobbying from Eastern European countries before the first new members were allowed to join in 1999. Even then, plenty of care was taken to signal to Russia that it was strictly seen as a defensive measure, from allowing the Russian government in as an observer at all levels, to limiting the military capacity of the Baltics and putting a very low cap on the number and type of NATO assets that could be deployed in countries bordering Russia.
The intellectual mistake that Chomsky and many who share his ideas make is to believe that just because Russia might reasonably feel aggrieved at no longer being able to politically and economically dominate the countries around it through the use of military force as it could as the USSR, that it somehow has a right to have that situation reversed and is therefore justified at launching an unprovoked attack on a neighbouring democratic country to gain back that power. There should be no such right in the modern era, and believing in it is a betrayal of traditional left-wing ideals.
Ironically, returning to a might-makes-right global order as envisioned by Russia would mean the United States could behave far worse in future, pulling off the same kinds of annexations and similar as it did as a young power, and when it was far less powerful than it is now.
It's also a complete mindfuck of a piece, with obvious cognitive distortions and major factual evasions flying from every paragraph.
But because it's expressed in that calm, authoritative, rational (sounding) voice -- and it's coming from Saint Chomsky after all -- "principled, internationalist" lefties eat it up like candy.
I admire Chomsky for other things he's done. But he's got a split personality also, and in some cases his "morals" are very deeply flawed.