Sorry it took me a while to respond. Been busy with other things, and since you had a workaround it didn't seem as urgent.
There is a bit of a dilemma here. These entries get added together with the 'DSL support' in an attempt to provide a better editor experience when editing .gradle files with the Greclipse editor.
Removing the 'GROOVY_SUPPORT' container will probably break some of the editor support at least for some projects.
So I'm reluctant to remove the container unconditionally.
Right now the container is only added to a project if the option to 'Enable DSL Support' is enabled.
So another way to get rid of the container is to not enable DSL support when you import a project.
This will also get rid of other 'foreign' classpath entries that are not really part of your project but put there to try and get a better editor experience with Greclipse, such as the DSL support classpath container entry.
By disabling DSL support, you are essentially saying that you rather have a 'correct' classpath for your project instead of extra cruft on the classpath put there to improve the experience editing .gradle files in your project.
I'm really not quite sure how to resolve this issue.