Sometimes this shows up when using auto quest add-ons, and there are no alternatives to make this message not show up when using said auto-quest add-ons. They show up each time the add-ons accept a quest and it is rather irritating to have to click it off.

Unfortunately this popup is due to some questionable code decisions by Blizzard itself; it's not the fault of any one addon. That particular dialog is also protected, so I can't make it go away with APR.

The best I can suggest is to get an addon called TaintLess. It helps reduce the number of times that popup happens, but it may not completely eliminate it. You just install it like any other addon, and it works silently; there's no options to configure or anything.