features designed to run in mojoPortal must run in the context of mojoPortal and jquery is already included in mojoPortal.
I don't really have advice for making a mojoPortal feature that also runs stand alone outside of mojoPortal. My advice is develop your feature for mojoPortal and test it running in the context of mojoPortal.
Perhaps you can use a web.config setting to control whether you load jquery and if it is running in your web app instead of mojoPortal then you can add jquery.