First, I always try to sign my spring training invites to a minor-league contract and not just an STI. Aside from that, there is probably a better solution than what I do if I don't sign the player to a minor-league deal: I cut the player and immediately sign him to a regular contract (usually minors). Because the player signed to an STI isn't on a regular contract (minors or majors), he just goes right to free agency and doesn't have to pass through waivers.
Again, there is probably a better solution than this, but it's just what I have found to work.