The fix for this, basically, is more instanced content.
Think back to Living World Season 1 - lots of open-world content. But when that chapter was done, that content had to go away for everyone. Because you've only got the one open-world.
This means that people who miss that content miss out entirely. You can't go back and re-play it like you can Season 2.
It'd certainly be possible to instance a lot of the content... Make all of Orr one big instance, and have it change dramatically after the cleansing...
But that winds up fragmenting both your users and your content. You now have to develop two (or more) maps for a single zone. And I'm not going to see the same content that my wife (for example) is.
World of Warcraft introduced "phasing" in their Wrath of the Lich King expansion to address just this issue. It allowed you to make permanent changes to the world. You could perform a quest to rescue a city, and it would actually stay rescued.
And it was a real pain in the ass.
I don't know how many times I tried to group-up with somebody only to discover that one of us was in a different phase. It became necessary to make sure that everyone was on the same stage of the quest/content. And it was very difficult to help people with quests/content you'd already done.
I'm sure there's various clever ways to overcome that... Hell, just let me right-click and "join X in Y" would probably do it... But then you're still magically teleporting your character into a version of Orr that hasn't been cleansed yet, even though you have cleansed it.
When you've got tons of people playing through content across the world, you've really only got two options.
Content only happens once, and then the world moves on. If you don't get there in time to experience the content you're simply left out.
Content is available for everyone to experience. Which means, ultimately, that you're going to run into some kind of continuity issues somewhere.