You mean the scuba has less than 1000psi in it, so it can't fill your bottle over 1000psi? Or do you mean that your tank can't give you 1000psi output from its regulator?
The mag valve can actually handle a very high pressure. That wouldn't be a problem. The problem would be the air lines going to the valve. You need the proper rated lines and fittings. The other problem you will run into if the scuba has more than 1000psi of unregulated air in it, is that the reactivity will be insane. The higher the pressure in the scuba, the greater the amount of reactive force put on the trigger.
If you have an inline regulator that can handle a high input pressure, you can regulate the output down to a stable usable value. Just connect the scuba to your tank. It will then use the tank regulator and be as if the paintball tank has a much larger volume.
Except for the Automag in front, its usually the man behind the equipment that counts.