The window-shooting bug on m02 exists in the vanilla game, and it does seem to be related to having upgraded weapons (via co-op). I have a small mod that helps people through it. It'll be in my troubleshooting collection post shortly. We'll probably want a more robust solution, though, one that doesn't just flip the "is the window broken" boolean check.
In mine, in the bonus section @ http://www.saintsrowmods.com/forum/index.php?threads/111/ , I just removed (commented out) the check for windshield damage. I'm too dumb to see what i'd need to change to make it not take away all your weapons on the start, I kinda like the idea of replaying missions with whatever loadout I have/want.
I suppose it'd be necessary to come up with a general "is this a replay?" check to put into lua files for stuff like this, though you could argue there's no harm with disabling the taking away of weapons for your initial playthrough.