It gives you an extra safety net, in case the version in the database would differ compared to the version in the VCS, even though they shouldn't, someone might have been evil behind your back. :)
PgDeploy lets you preview the change and show you a diff.
If the diff is expected, you can proceed and deploy.
Only if your workflow is bad and you're editing stuff directly on the DB. Stored procedures work fine with VCS if you write them on files and then run those. Where I work, creating a new database with all the procedures is just a matter of loading the right .sql file.
