Apparently GPE compiles GWT modules in the module list found in Project Properties --> Google --> Web Toolkit so removing modules from there did the trick. I was expecting to find either a way to select GWT modules from the GAE Deployment Dialog or to edit some configuration file.
It has to be admitted that relying on such GPE settings is not a great way to make consistent deployments. Maven-based builds and deployments made outside of Eclipse are likely a better way to go.