From the shack news source, they used the key words 'being escorted out of the building', which makes me believe they didn't leave on good terms.
Usually if your higher-ups are leaving in a positive/amicable manner, they make a press release saying something to the effect of they appreciated their work during their tenure and wish the best of luck in their future endeavors. This just sounds like a straight up canning process.
Also very curious why these guys would leave. Was Nintendo forcing them to remake an old franchise and these guys wanted to do something new? or was it that they just wanted to go separate ways.
Knowing Nintendo, we'll probably never, ever know the whole story.