I really don't see the problem here.
Even if he sticks with the mapping options from LC1 I don't see the problem. I found the mapping layout explanations to be fine then.
Of course, everyone's got their own thoughts and opinions, but even then Mig would just be tearing his hair out if he tried to make a setup that made everybody happy. That's not gonna happen. Somebody's gonna have a problem with it regardless of what he does.
And all the same, I don't necessarily think it's the doom of the game (like you're treating it) if he doesn't have it that way. Unless the playerbase suddenly suffers massive IQ drops and becomes too stupid to figure out the controls by pressing buttons and seeing which does what, I don't think it's that big an issue if the controls mapping setup isn't detailed down to the tiniest aspect.
Certainly a really stupid thing to "distrust" the project over, though. I'm sure Mig and crew really appreciate the notion that every other aspect of hard work they've done clearly doesn't matter at all since the control options setup seems to determine how good or bad the game is. How silly they must feel having done all that work, only for people to inherently doubt and mistrust their game's quality all because the setup for controls isn't "right."
If the sarcasm's not sinking in (entirely possible, tone and text and all that), I'm basically saying it's a valid thing to be concerned about, but playing it off like everyone's gonna just doubt and dislike and not trust the value of the entire project because of it is stupid. It'd have to be on-par with Jekyll and Hyde NES or E.T. Atari in terms of shittiness for it to hold the amount of weight you're acting like it does.