I don't know of a way to exclude certain files using the command line plugin. Maybe you can try using m2eclipse instead of the command line plugin.
Well it's not really a big deal excluding those files. But do you know if it is possible to make the eclipse plugin to make Eclipse output the classes somewhere else than target/classes? It is a bit annoying having them there since every time I do a "mvn clean", a full rebuild is needed in eclipse.
$mvn eclipse:eclipse -DbuildOutputDirectory=eclipse-output
but that did not seem to have any effect