Users nor MOD tables will make up the majority of the size of the DB. For example, I have a populated test board with 10,000 dummy users. The user table is around 6MB in size. The mass information in the database will be occupied by the _posts and the 3 _search tables, all of which are several hundred MB.
There also may be lingering overhead on active and large tables, which can be recovered by optimizing
the tables. This all depends on each individual board. I highly doubt cleaning up the MODs from the database will reduce the size of the DB to any significant amount.
At this moment in time, the STK is still in the testing stages and should not
be used on a production board. Because of this, there is no "official" way to clean out the database of all non-vanilla tables and fields.
However, as has been said, deleting/replacing the files as was explained in my post above will remove any/all traces of the MODs from the files, and the tables in the DB will never be touched again. If you still want to remove the tables at a future time, the STK is working to be released as soon as possible.