The normal way is to get a spot welder drill. It has a pilot bit and a cutter and you drill through both pieces of metal with the pilot bit. When the cutter bit starts cutting you only go through the first layer of metal. This is about the only way you can do it neatly. Standard fixture in the auto body shop buisiness to remove spot welded panels etc.
Your problem may be getting one large enough for your job. If you have the room you might be able to just drill through them. Your outside area of cut must go past the edges of the weld to separate the two pieces of metal.