Allen screws are only holding the rotor on the hub. If you're worried about bending the disc you can remove them but I warn you they may be stuck in and you may end up stripping them out, I know I have before.
It's designed to slide off, at least it is on the other Yamahas I've owned. More than likely it's stuck on there, and liberal application of lubricants or some time with the torch to heat it up may be in order.