WP is designed to use a single database. In fact you can have several sites in a single database because they’d each use a different table prefix.
How difficult it’ll be to cleanup will depend on the code involved. I’d be mostly concerned that since the previous developer (I use the term loosely) didn’t use WordPress coding standards, they likely used older PHP standards if any at all, and the databases may be accessed with the older, deprecated, mysql_* library.
Yes, if it’s not going to be a lot of trouble to do so, I’d definitely rebuild from the ground up.