If it's DBW (06+ sti) you will loose cruise control. If its cable throttle you should be able to keep it.
Even though the
ECU controls the throttle on a DBW car, there is a lot of checking and redundancy in built to make sure the pedal position matches the throttle position. Cruise control would require this to be bypassed and this is deemed to be too much of a risk. No one wants their car to go full throttle all of a sudden when they're not expecting it.