I have Aptana Studio 3.6.0 installed on Luna 4.4.2 (running on Ubuntu 15.04 64 bit). Aptana bundles in a considerably old version of PyDev (3.0.0) that is largely non functional
The short answer: no, PyDev can not be unbundled from Aptana. The Aptana plug-in should not be installed on Eclipse Luna.
The long answer: the Aptana plug-in available for Eclipse Luna not only ships with a non-functional version of PyDev, it also breaks various things in Eclipse. I finally quit Aptana yesterday, I just could not continue working without PyDev. After that a number of issues that I thought were bugs with Eclipse suddenly become functional again (e.g. current line highlight, Colour Theme). I wish I had removed Aptana sooner.