When you create a project, you choose which drive to place that project onto. That project is a folder hierarchy and the DV content you are importing should end up in that project folder. So, if that project is on the external drive, then I don't understand why you would get the error. Perhaps there is some overhead occurring that uses the internal drive, but I don't think so.
So, if you can navigate in the Finder to the external drive and see your project there, then your only option would seem to be to clean up your internal drive a bit. OS X it self needs some breathing room on its startup drive.
One last ditch option might be to remove the iMovie preferences file and see if that somehow (magically) fixes the problem when it is automatically recreated.