Actually the spacecraft being so far away was the reason to put some Lisp system on it. That was one goal of that mission. The software controlled the spacecraft and did not need detailed programs what to do. It would figure out what to do from higher-level task descriptions and what it sensed. Basically a spacecraft as a semi-autonomous robot. Since it was running on top of Lisp, actually LispWorks, it could also be debugged/reprogrammed at a lower level.
I shared the reaction, "wow, must've been glacially slow"