I imagine that when Notch made a deal with Microsoft, he stipulated that Minecraft can still be released on other systems. I'm guessing that Microsoft just own Mojang in so much that they get the lion's share of the profits. Otherwise it would be in their best interest to ensure Minecraft remains exclusive to their own platforms. I freely admit that this is speculation, however.
But let's also consider the fact that Banjo and Kazooie appeared as guest characters in Sonic & Sega All-Stars Racing, but only the XBox 360 version. If Microsoft weren't going to let their characters appear as a guests in the Wii version of a multiplatform game, they certainly aren't going to hand over entire games that are a big selling point of Rare Replay.
But the most telling thing of all is simply that these games are absent from the Virtual Console. I don't know why people think they'd be any more likely to appear in a N64 mini.