The whole point of bringing in SK at Nintendo was to cover the gaps Nintendo themselves left. This idea that they parted ways because they share different philosophies is therefore ridiculous, that was the whole point of them being there in the first place.
Who knows though, maybe that's what Nintendo really told Dyack. What they actually meant of course was that their games are selling like shit even when they got a big franchise and, amongst fans at least (not so much reviewers), their titles receieved very mixed reactions.