Is pseudonymous publication ethical?

The worth of scientific work is in the content, not in who wrote it. Therefore, I think publishing under a pseudonym is not necessarily unethical. In the example the OP presented the author was prevented from publishing if he used his own name. If the research was sound and reproducible, I would be fine with this. In practice I would like to know who wrote the paper.

I don't think there's an absolute answer here. Ethical questions generally have lots of "grey areas" associated with them.

I think the biggest question to ask—and the one you indirectly are headed toward—is "why is someone using a pseudonym?" If the answer is "to get around a contractual agreement that both parties have agreed to and accepted," then it's likely that the use of a pseudonym is probably unethical. (Although one could argue that if this were intended to "correct" a more serious problem, then it might still be ethical—even if contractually messy.)

If, on the other hand, the answer is "to avoid potential review bias," or "because publishing under one's own name would make one's life less convenient" (for instance, there's a negative stigma associated with publishing outside one's "home" field), then it's less clear that there's an ethical violation in progress.