It's 20+ years since I've read that, but as you describe it there was no choice between evils in the most literal sense: as in, Batman did not do an evil thing in not rescuing A - and he did a good thing in not rescuing B. The situation falls short of the idea - of A and B both being rescued - but Batman has not committed an evil.
Contrast, say, Batman shooting A so as to rescue B. That would be committing an evil, assuming a standard non-consequentialist morality. In any non-consequentialist morality the nature of the acts that the agent performs, and of what she is responsible for, is fundamental. Diffrences between acts and omissions; intervening volutnary acts of others; and the like are all crucial.