It sounds, personally, like there's actually two primary stages to this process. Standard and Custom. Right now they're rolled into one.

What I would recommend you do is create a standard 'cleansing' protocol. This would be a primary load location (or a series of scripts deployed to the database that you've just built via Model) that would take care of all standard cleanup components.

Then, customs would be ran after the standard, hopefully keeping what's standard from now on and what's custom per client/data component separate.

Also, you might think about giving your users DDLAdmin on the databases so they can deploy their scripts as procs so you can more easily keep track of what belongs to whom. My guess is this is the way it's easiest for business because they've never been shown an alternative.

However, really, that's a big deal you're dealing with over there and it sounds like that's their primary source of revenue, at least for the department you're supporting. I'd tread lightly and first learn their process before you go and start making major alterations.