Disabling the "run" button for a few seconds was actually done to mitigate another risk -- sites cueing the user to click in a particular location, then triggering the confirmation dialog with the "run" button right where the user was about to click.
I have to type "danger" to bypass this restriction, and I thought it was pretty cool.
Another good UI pattern is in Firefox, that it disables the Run button on downloads for a few seconds.