The problem is that the players aren't in a position to refuse, because the core premise of the game is that they have to band together on this ship. This player was taking advantage of the meta-context to take the resources that were allotted to the other players in character creation, with no potential recourse other than exiting or breaking the campaign.
I'm surprised that no one has said this yet, as far as I can tell. Part of the issue here is that massive-scale events like these are not realistically optional. Any faintly good-aligned character is morally obligated to engage with a preventable danger that threatens millions or billions of people. A counterpoint is that if they don't want to be morally obligated to do things, they should have made a hardline selfish character, but that's just not a reasonable expectation. If you want players to play actual characters, you have to accept that what the player cares about and what the character cares about will not automatically align, and that it's inevitably the DM's responsibility to make what the character cares about not boring to the player.
In fact, you say you don’t run plots, but I’m confused about what you think a plot is, because this kind of important event that is difficult to justify not participating in is exactly what I would call a plot.