Unless Y2K comes before 1989 it most certainly did not come from Counter-strike. Pwning something had existed throughout the 1990's hacker culture and likely was in use in the 80's too. There are some of us old enough to remember it being used. It probably stemmed from QWERTY keyboards and o/p being close to one another. "Pwned" is an easy typo from "Owned" and "owned by [some hacker/hacker group]" was always common way to deface hacked websites. It easily predates Counter-strike's release date by at least a decade so it could not have originated from CS.
How about trying to search through all the Phrack articles to find the use of the word "pwn" that doesn't refer to Phrack World News? Spoiler alert: you won't find any usage of "pwn" or "pwned" until well past 2000. If it was so much part of hacker culture you would have seen a reference in the earlier articles, but you don't.
That being said, it probably originated as a typo and that could have happened on multiple occasions.
Hack/phreak BBS culture and leetspeak went mainstream though IRC and video game chat.
Everything old is new again, nothing new under the sun, etc.
I'm waiting for !!1!!!1!11 to make a resurgence.