Similar to what is available for "reset-mod-settings"; but add a "disable selected" option.
As you can see in the screenshot, it's clearly indicated which mod caused the issue; I would like to selectively disable that mod, and relaunch the game.
+1 as it's annoying when the game insists on disabling everything else that touches the prototype even though you know for sure from the error message which mod has to be the offender.