The line out of the top is the most likely candidate for being the supply line. Old units used to have the circulator on the return line to save the seals from hot water.
The best way to remove the pipe is the way that works best for what you intend. Cutting the lines with a saw that can cut flush to the floor is one way. But it would seem you need to have the old pipe removed to below the floor level to be able to refinish. Many times a large pipe wrench will either unscrew the pipe or break the threads. If the pipe is truly cast iron, then breaking the elbows with a heavy hammer is another way. At times heating a joint breaks the rust, and sometimes cutting with oxyacetylene is necessary.