Yes, one has to marvel at the stupidity and incompetence of Commodore Marketing. Besides the PET in the first movie, William Shatner had done some Commodore Vic 20 advertisements a couple years earlier. So you think it would have made sense to continue the Star Trek association - and it only would have cost the price of one Amiga. This is just one small example of the many stupid screwups of Commodore Marketing.
I don't think it would have had much long term impact though. Seeing the computer in the movie didn't make me want to buy a Mac at the time - even though I was obsessed with new computers back then. I didn't even notice it was a Mac until 10 years after first seeing the movie. It's not like Scottie spent half an hour with it and said "Gee, this computer's a fine thing... much better than the flashing crap-boxes we got on the Enterprise. What's it called again? A Mac... what a bonny name! I'll tell you what... throw in a couple Macs with the deal and I'll also give you the secret to 'edible underwear'."
