I use the LRTimelapse time lapse templates (see the mid-page of http://lrtimelapse.com/download/
I shoot RAW (maybe in Med RAW or Small RAW), copy the files from the camera to an external USB 3.0 drive, adjust the flicker (if necessary) in LRTimelapse, modify the batch in Lightroom, then export as a video using the highest quality template (I may have modified it to be slightly higher bit rates for non-web videos). No JPGs necessary. I'd think this method would also be faster in the long run.
Without external hard drives, shooting RAW would be impractical for me. I rarely keep RAW files on my computer. In general, I keep at least one copy on an external, and try to have a second backup of the more precious ones on DVDs, along with the Lightroom files.