Yes: I can't think of a design where this would cause a problem. Historic and traditional organs (slider or pallet) would be fine since the key action is completely independent of the stop action. I can't think of any organ that would actually be damaged by pulling stops while the keys are depressed. Nor can I imagine anyone would be content to keep repairing the damage that would inevitably ensue.
Maybe some early 20th century cinema and extension (unit chest) designs might have done something unexpected - they did some crazy things with electromechanical relays as they were discovering how to use them.
EDIT: On reflection, your question might be about couplers rather than stops. The designs of inter-manual, octave and manual-to-pedal mechanical couplers used for the last 250 years have allowed them to be brought into use easily and safely while keys are depressed. (They may or may not have any effect on these notes depending on mechanism). Before that, this was not always true: it took some time for workable designs to emerge.