Hey,
I dunno if you got an answer to this question or not but I had the same issue and found a loop hole.
You need to go back into iTunes and choose the Photos Tab.
Under that, it should give you an option to Sync Photos. When you select that option, it gives you the option to either:
-All folders
-Selected Folders
-Include Videos
I chose the Selected Folders option and chose NONE of the folders that popped up in the box below (so all the boxes were unchecked). Then I hit either Apply or Sync and it took all the picture folders that I had downloaded from my computer off my phone, leaving me just the camera roll and my photo stream.
If you figured this out already, then congrats but if not, it worked for me so it may work for you and you can try it out worst case scenario, someone who will Google it one day and see this and it could help them out).