I don't understand the difference between having your character mutated at the very start of the game via plot and having him mutated during the campaign via plot. What if the PCs woke up on up in an MA setting but no one had mutated, but when they left the stasis room they were exposed to radiation that did mutate one of them? Or if simply stepping out of their stasis pods could mutate them? Or take it in the other direction, and 10 sessions into the campaign your character mutates.
On the one hand, a player might feel that if the mutation happened as a result of the plot during play, at least he had a chance to influence the direction of the plot. Maybe he didn't want it to happen, maybe he wasn't able to escape the unwanted fate, but if at least he could see it coming and had an opportunity to
try to avoid it, I'd think it'd be okay.
On the other hand, if the change is going to come as a result of DM fiat as in the OP, I would personally prefer it to happen at the very beginning of the campaign. That's true for a character change or for a genre switch. As a player I would be much more likely to take it badly if the DM told us, "When you wake up after the last adventure something has happened, everybody has guns instead of swords, and also you've mutated" - yeah, presumably having invested myself in the setting and my character to this point, it'd be pretty hard to swallow. Having only gone so far as to create a character, on the other hand, I think I'd have a lot easier time rolling with it and seeing how it plays out.
If the DM plays with my expectations once at the start for a surprise, I can enjoy the surprise. If the DM does it after things have been set for a while, it will make it harder to trust him.
I think a lot of this discussion may be colored by experiences people may have had with power-tripping players and DMs. It's reasonable for a player to want to keep control over his PC's identity and "crunch", but sometimes players can be unreasonable, objecting to any change that might impact their character (no matter how indirectly). It's reasonable for a DM to try to mix things up, including sometimes changing something that affects the mechanics of a player character, but sometimes DMs can take that too far, trying to teach players "who's boss" by pulling the rug out from under them.
As always, communication is key. In this case, I think the DM would have been wise to sound out the player about possible changes to the PC, not necessarily giving things away - "hey, would you be averse to a little surprise where your character might turn out a little different than you planned?" And then leaving the door open for the player to make a new character or otherwise recover if he ends up really unhappy.