There is no good or "right" way to deal with iPhone videos.
This is a big problem Apple needs to address.
I currently suggest keeping them in iPhoto along with the photos from the same month, but as you've seen, iCloud makes this a pain in the ass. You can either stop using Photostream (and just import photos and videos together with USB) or you can hunt and peck and carefully import the videos from your phone without picking the photos during import.
Neither solution is ideal.
And then add to that the fact that Apple apparently wants you to store "Home Movies" in iTunes (since that's the only way to sync them BACK to the iPhone should you want to do that), but gives you no direct, easy method to get them in there.
All of this adds up to one big mystery: Just what DOES Apple expect you to do with home movies?