I've not had this problem using iPhoto on the Mac to import the photos. This could be an interaction between the iPhone/TimeLapse and Premiere. Do you have this problem with photos taken with the camera manually?
To delete the photos on the iPhone you use the same method you would use to delete photos imported directly from any camera (assuming you are not pulling out SD cards). Namely, when importing the photos, there should be an option to delete them on the camera after they are imported.