We don't know...but we also don't know if Sakurai would just accept whatever they suggest afterwards. If he contacted them with the purpose of getting Banjo & Kazooie I'm not really convinced he would change direction and go with a Halo or Minecraft character just because Microsoft disagreed with him. Think about it, if he did go to Microsoft with the aim of adding Banjo & Kazooie as a playable character, then he's not looking for a "relevant" or "blockbuster" character like Master Chief or Steve.
It's like if Sakurai went to Square Enix asking for Cloud and they suggested Lightning or the latest Final Fantasy protagonist instead, would he have gone with it? Who knows but I'd like to think he wouldn't put a character in the game just because a third party said it was a deal breaker.
I'd like to think Sakurai sticks to his guns on this sort of thing....but yeah we don't really know what would happen in that scenario. (which is why we're speculating
)