Sure. If there were any ambiguity as to the orientation of his morality, or if she were more disconnected from the situation, then certainly it would be even the expected decision.
But those are both big 'ifs', that don't happen to apply. If everything is as it seems, then I think she'll have been in the wrong, or at least overly reactionary. It should cause a rift in their relationship, regardless of what moral judgement you want to make on it. But I'm not against that, necessarily -- so long as it's handled with aplomb. Lois considering what her duty was, as both a friend to Clark and Superman, with Superman's obvious sphere of exceptionalism should extend over the boundary of his identity, whether her motivation was pure, or whether some of it might have come from the pain of discovering a lie, or the desire for the notoriety that comes from breaking the biggest story of the 21st century...and for Superman, too, to ask those questions, to question is moral right to live a lie amongst those he ostensibly trusts, and who he asks to trust him implicitly with the power to destroy the world many times over.
Good story is good story. None of these decisions are wrong, in a vacuum.