Looking at the STS Maven integration, it does appear that the Spring Project Configurator will automatically add the Spring nature if it finds the Spring Framework dependency declared in the pom. Maybe that should be user configurable?
It sounds like you have two issues: 1.) STS is automatically adding the Spring nature to your Maven-ized Spring projects and 2.) STS build is too slow when you have many Spring config files enabled for Spring tooling support.
Leo Dos Santos
Committer, SpringSource Tool Suite