How can I make iMovie delete videos from my iPhone after importing them?
I don't think you can, but you can delete them using Image Capture!

Image Capture lives in your Applications folder and can show the contents of a camera (or your iPhone's camera roll) as a list, and you can manipulate it directly, including deleting some or all of it. I'd just pull up Image Capture after your import, and then sort by kind to isolate the movies, and delete the items you just imported.