This is all moot and academic anyway because of the first point, yes (and because it's not like CN:S will get a rep or even an Assist). As for the second, while NoA certainly realized they could no longer boast about the game's all-star cast of sci-fi TV alumni as they clearly hoped to do, for reasons they couldn't have foreseen when the contracts were signed, I don't remember the casting being actively suppressed. I followed the game closely and nobody paid any attention to the cast (including Wil Wheaton or Michael Dorn) until the demo was in the wild, partly as there was little attention to the title to begin with. As I recall, this all truly blew up when it attracted the notice of people who were watching Baldwin but not the game, when he promoted his own involvement in it on the eve of release, although the demo had been out for weeks and his involvement was already a matter of public record.
Obviously there is a strong disincentive now to attract negative publicity with Baldwin's name, and I see he hasn't had any recent voice credits in games, but I think we're mostly resting on our own assumptions here when we surmise he'll never be asked to reprise a role. We don't know that his working relationship with Nintendo was ever anything but professional, so blacklisting him is purely a question of media blowback, if an important one. It's a tough spot for Nintendo to be in, though I don't particularly care if he comes back or not (VAs for long-running characters change all the time; big deal), so long as the IP gets another chance in some form.