Very much agreed. In GeoTools and GeoServer projects we would like to use a separate Eclipse output directory but at the moment it's not possible due to this very issue, as we have test resources that do overwrite main resources with the same name. Both are related to the respective plugin systems, which look for a certain file in the jars, and the tests, that in order to double check the plugin system itself, use files with the same name to install test plugins.
The separateOutputs.patch file is a trivial patch that makes it so the output of src and test end up in different directories fixing the problem for us. The intent is to consider the outputDirectory not as the directory where the classes will be put, but as the root for the main and source output directories, which will be kept separate. When the outputDirectory is set to $OUTPUT, the main sources and resources will be targeted to $OUTPUT/classes, whilst the test ones to $OUTPUT/test-classes.
If this behaviour change is not acceptable I'm ready to prepare a patch that will add a testOutputDirectory parameter instead.
Oh, I coded the patch against the 2.7 releases sources.