There was a previous bug opened and closed for this: 3024004
In short, trying to install pyDev via the eclipse or equinox command line results in a failure that can not be worked around. The root of the problem is the untrusted certificates that pyDev is signed with. There's plenty of reasons to install via command-line, but in our case we're building development environments with a preconfigured group of addons. The Eclipse IDE is never started in this process; it's all machine based.
I believe the benefits of signing with untrusted certificates does not outweigh the cost. If you remove the signing for now, you may be able to begin signing it again once equinox better supports untrusted certs.
Output and error:
Command-line arguments: -os linux -ws gtk -arch x86 -D osgi.support.signature.verify=false -consolelog -application org.eclipse.equinox.p2.director -repository http://pydev.org/updates,http://download.eclipse.org/releases/helios -installiu org.python.pydev.feature.feature.group
!ENTRY org.eclipse.equinox.p2.engine 8 0 2010-10-28 16:59:27.828
!MESSAGE One or more certificates rejected. Cannot proceed with installation.