Eliezer did say "Doing worse with more knowledge means you are doing something very wrong," but check what he said in the very next paragraph: "On the other hand, if you are only half-a-rationalist, you can easily do worse with more knowledge."

The solution to this problem is do something Eliezer always argues against for some reason, namely, to compartmentalize.

Also it's likely that becoming more rational won't necessarily help the reasons you mentioned here.