If you're making that decision against their will, than yes, you are. Consider Prohibition. That was ostensibly done "for the own good" of the American people.
"Yes, you are" what? Being malicious? Prohibition may have been wrong-headed, but it wasn't malicious. Do you think it was?
In any case, an impersonal, one-size-fits-all government edict has little to do with relationship decisions made between brilliant and empathetic intimates. Bean obviously knew more about what Petra wants and needs than any government ever would, and cares more for her welfare and happiness, too. Governments don't feel the pain they cause their subjects as Bean felt his beloved spouse's pain. There's no good basis for a metaphor here. Staging an intervention would be a better metaphor, but it doesn't help your argument; an intervention isn't malicious, either.
Psudo: I'm not saying he can't break of the relationship, but it is obvious that his reasoning was not because he felt he was being treated unfairly, but because he didn't want to deal with his own personal guilt over a decision she would have made.
Whether he feels unfairly treated is exactly as irrelevant as whether she does. Neither is entitled to fairness (as the crappy, unfair moments of their lives demonstrate), nor are their feelings necessarily accurate gauges of whether they receive it. Petra's belief that it is unfair doesn't make it so, nor does unfairness prove Bean's decision immoral even if it did.
The fact that someone's self-determination is thwarted either way proves that it self-determination is a lousy standard, but it remains a lousy standard whether Bean feels slighted or not.
Feelings themselves are a better standard; at least feelings weigh differently on Bean and Petra and both depending on whether Bean leaves or not. They are both, individually and together, less happy if Bean leaves. That is true regardless of whether they have or are entitled to fairness. If you want to condemn his leaving on those grounds, be my guest. It's a remarkably healthy kind of hedonism, to want to protect family unity and remain with your beloved spouse and to love and be loved. I can't confidently oppose it. Maybe Bean should stay.
Bean, by nature, doesn't trust feelings. He looks at concrete, physical differences in the world, and he prefers the physical consequences of leaving to those of staying. He makes a strong case for it. Should it be demanded that he reject his nature so that Petra can indulge hers? Is that fair? Maybe Bean should leave.
I don't have a final answer. If pressed, I'll say "Maybe."
But self-determination proves nothing here. Fairness is a more complex issue, but I doubt it proves anything here either.