While I agree that anyone who wishes to kill a deer can use whatever he/she has with them, I think the logic behind the rule goes more like this:
Someone who is out deer hunting will be using a caliber that is large enough for a sure, one shot kill.
Walking thru the woods carrying a larger bore gun and planning on shooting a deer out of season or without a permit, if he is stopped by the G&F officer he'll just say, "I was just out squirrel hunting with this.
No, I always use my .54 for squirrels. It saves having to clean them."
Now, while I know the members here are smart enough to not try to pull that trick, there are a whole lot of stupid people out there.