Absolutely, but he isn't the sole author: https://github.com/ovity/octotree/graphs/contributors
I'd imagine that he knows this, which is why he's pretending that the proprietary Octotree is a "complete rewrite".
From your link the contributions do not look huge so it seems that removing them is quite doable.
Example: https://github.com/christianbundy/octotree/issues/1#issuecom...
If the maintainer wants to remove the AGPL without copyright infringement, I think they'd need to delete most/all of pjax.js and have someone else write a clean-room implementation that isn't built on contributions from someone else.
The reason people do cleanroom is to eliminate risk of liability, it's simple, and it's foolproof. You can't mess it up. It also eliminates other potential issues (like tortious interference with someone who signed an NDA).
Legally, it's overkill. It's like using a thermonuclear bomb to swat a fly.
If you're going up against Microsoft, overkill absolutely makes sense; you might be legally right, but it will take millions of dollars in legal fees to show that. Programmers are cheaper than lawyers.
In the general case, though, you can just rewrite the old code and be done with it. Yourself. Looking at the old code too, so long as you don't borrow it. You want to be a little bit careful since it's not just the literal words (you can break copyright on a novel if you rewrite the same plot in your own words; same thing with code), but "a little careful" suffices.
It's a bit harder to transform a piece of code into something non-infringing, rewriting section-by-section, but most lawyers say that's not impossible either.
(Of course, clearly, none of that happened in this case)