One might ask DavidW if he's willing to update SCS, but he seems to be busy... and it's not a bug with SCS... wouldn't that be something to be implemented for example into the BG2Fixpack, necessary for everyone?
I guess if you don't like certain mods you'll have to uninstall everything, install again (minus the "bad" mods) and start a new game. Anyway, I would always recommed first to have a look what one is actually installing to prevent such problems. More mods=more changes...
The installation itself is not affected. If during the download process somethings goes awry, just download the mod by yourself. The linklist can be found here: