Well, with the Famicom and Super Famicom Disc-system, Nintendo already had experience with using discs as a storage medium for games. I guess they wanted to give it another try with Sony as partner, seeing how Sony had a lot of experience in the multimedia branch. Maybe Nintendo didn't want to continue with it because of loading times or something? Whatever be of it, if it was going to be good for Nintendo, they would've continued it. I guess Sony did see a future for it and agreed with Nintendo to go separate ways.
And that was quite possibly Nintendo's worst move in the history of gaming. They indirectly spawned a competitor that would become the gaming giant of modern times.