Luis,
I can answer this one. Organs had been sampled for use in non-realtime playback systems since at least the 50s. You can learn about this by searching for "computer music" online. It was a quirky era.
The first sampled real-time organ was the concept system that North American Aviation built in the mid 1960s. It used a crude plug-in diode array to enter three stops from pre-determined wave shapes - by hand. Then the three stops could be drawn to play them on a single manual. This was the instrument that was shown to many US organ companies. Only one of these companies, Allen Organ, saw the musical and economic potential in the system. This led to a partnership between North American and Allen that produced the first commercial digital organ in 1971. We had a fully-functional prototype of the organ in our home for a year or so before that, and I practiced on it daily.
Allen was defintely the artistic force behind the first organ. They were not trying to reproduce a specific existing pipe organ - but rather wanted to provide a comprehensive 2-manual instrument for the organ literature.
The only reason these first digital organs were not software-based is that the general purpose computers of the time could not handle the necessary computational rate. The first generation Allen system used custom microelectronics provided by North American (which soon became Rockwell after a merger.)
You can read more about this on my web site here:
http://www.nightbloomingjazzmen.com/Ralph_Deutsch_Intro.html
Les