Saying that hypothetical cleansed Orrian undead would join Joko just because he's the strongest undead power would be like saying that Kryta would happily let itself be absorbed into Cantha because that's the biggest human nation, even if modern Cantha was so despotic that it made Usoku's Cantha look like a beacon of freedom and racial tolerance. Just because they're both undead doesn't mean they have anything else in common.This goes double when you consider that it's going to be the Pact that would be undertaking this mass cleansing if it did happen, and the Order of Whispers is hardly going to let all that effort join the ranks of the enemy they were initially formed to fight. Keep in mind that despite their broadened perspective, the Order started as Turai's spy ring, and according to the Movement they're still working to oppose Joko in Elona even now.
Never said they would join him by choice.
He is an extremely powerful undead lich with power over other undead. Who's to say he couldn't take control of them by force adding their dizable forces to his own.
In one of the arah explorable paths we learn that the dragons control over their minions can be removed, thus freeing the minnion but allowing them to keep all their new traits/abilities. The test subject this is found out on is an undead chicken, which is then adopted by a cheerful pact member who is a Sylvari.