Unfortunately there's no way to do that without hacking. All the module is doing is pressing and holding the button like if you were doing it for 15 seconds, so the windows going up is a built-in function.
However, this is not a big deal. All you have to do is as soon as the top finishes going down (you'll see the red light turn off in the center console), press the two buttons to make the windows go down. They'll go down without issue and stay that way.