How can I safely remove one baseboard heater out of a set of two?
If you remove one, the other may not be able to handle the heating demand. This could lead to a cold room, and/or a shortened life of the heater. 

If you still want to proceed. Shut off the breaker, and disconnect the second heater as close to the breaker as you can. Don't just cut the wires, disconnect them at a splice point inside a junction box. Cap all the wires with twist on connectors, and label them so future owners know what they are.

If you have another source of heat, and would like to remove both heaters. Simply shut off the breaker, and remove the circuit wires from the panel. Coil the extra wire up and wrap it with tape, then label it so future owners know what it is. Remove the breaker from the panel, and fill the hole in the cover with a proper filler plate.

As usual, if you are not comfortable with electrical work. Please contact a licensed Electrician.