I use IntelliJ so I am far from knowledgable when it comes to eclipse, but maven should copy its class and resource files to target/classes (the default value for build/outputDirectory) regardless of IDE being used.  I just tried running a maven package in eclipse using the m2e plugin and this was the case.  The m2e documentation also seems to indicate this: http://wiki.eclipse.org/M2E_FAQ#How_to_configure_Maven_project_to_use_separate_output_folders_in_Eclipse

I think this stackoverflow post explains if you don't import a maven project correctly to start with, you will get a bin folder: http://stackoverflow.com/questions/13853902/eclipse-m2e-update-maven-project-adds-an-unneeded-bin-directory

Thoughts?