Actually on my to-do list is to include a manual uninstall script for all our modules. however, it won't be part and parcel of the automated uninstall for the above reasons. We've just seen it happen too many times that a user thinks they should uninstall prior to upgrading. Keep in mind that we still have customers on DNN 2.x before anyone says well the last version of DNN...etc,etc.. so we have to take those people into account with any change to the build procedures.
Recovering from a "uninstalled" module is tough enough, but at least the user does not lose data, but it usually requires us to get in there and make sure things are okay. From the end customer point of view (being the site's customers) at least they still see their orders at the end of the day.
The way I look at it, there's nothing worse than having to say to a client "you're restoring from backup, buddy..."
Each developer though has their own mentality on this, and some of our modules need to be cleaned up in this regard, but the larger ones where the accidents could be disasterous, it doesn't make any prudent sense to auto-uninstall. ie: sitetrack, emailmanager, portalstore and support desk.
As far as the prompts, how many times has a human been distracted in hit Yes instead of No on a delete? :P me personally? undelete is my friend at times :)
Cheers,
Richard