It depends on whether your tractor has a self-bleeding fuel system. I'm sure you could find out in your manual somewhere. It probably does since even my JD790 had an electric fuel pump to prime the system. So if you ran out of fuel and the engine quit...just put more fuel in, turn the key on, and the electric pump should prime the system. It did say in my manual something about might have to crank the engine over longer than normal.
If it's not self bleeding you have to bleed the air out of the line - there's usually the procedure for that in the manual too if your tractor is not self bleeding...
As for whether it is hard on a tractor, I would say no way! My reasoning is, to shut the thing off normally all you are doing is depriving it of fuel, so as far as the engine is concerned, I would think it would be the same as if you turned the key off.