Hey there BW this is what I think of how you should change Flashpoint loot.
When an ORANGE item drops that is let's say "medium armor" I believe only medium armor wearing classes should be able to roll for it, but keep it so you can trade it between party members.
This way People that actually need the item so they can make use of it, can get the item and not some sorcerer who decides he wants to take the medium armor jacket... doesn't matter if it's for a companion. This will make sure people don't ninja items, but also if the medium armor wearer already has it or doesn't want it, he can then give it to the sorcerer and his/her companion. I know these loot aren't so important but some of them are great for cosmetic and leveling purposes.