It would be unusual for an aux trigger input to present 50 Ohms resistance as a load. You can measure it easily with a Ohm meter, if it measures 50 Ohms across the input you probably only need to add a series resistor to limit the GPIO current to a safe level. If the resistance is much higher, still add a small resistance (~47 Ohms) to give a degree of isolation if the input presents a capacitive load. If you are using screened cable, put the resistor at the GPIO pin, not at the scope end of the cable. Most aux trigger inputs only need a small signal to work on, when your scope is set to aux trigger mode you should be able to set the trigger level so it is sensitive to quite small voltages.
Brian.