I think that's a bit excessive.
What he said was stupid, but as things that damage the image of U.S. companies go, Nadella's comments are the most recent example-- not the most offensive or concerning.
I share your thought that more people should think about the ideals they tacitly support when they purchase certain products, but...
Nadella said something stupid. We can only guess at how his ill-chosen words actually align with his intent as a chief executive. We live in a culture with a lot of systemic biases, as well as a strange indifference to the way language normalizes these prejudiced structures. For that reason, I think it's positive that Nadella's been taken to task for perpetuating such a bad point of view. But you seem to expect him to simply fall on his sword, as though there is no way he could possibly atone for 45 seconds of poorly-chosen words. If additional evidence of pay bias against women under his tenure as CEO comes to light, then things might be different. But so far as we can tell, for the period he's been CEO, Microsoft has increased the percentage of its workforce that it made up by women, and also increased the percentage of leadership roles occupied by women. The company's ratios are still disappointingly skewed toward men, but the point remains-- the company has become more diverse since Nadella's been in charge. We don't know anything about pay equity, and we can't be sure how much direct influence Nadella's had over the change in workforce demographics. But that's sort of my point-- there's a lot we don't know, and what we do know certainly doesn't necessitate that he resign. It demands that he apologize, and that he pursue policies that show he's taking the issue seriously and thoughtfully. I'm not defending the point of view he expressed, and I think his statement deserved to be addressed-- but perspective is important. It's emotionally satisfying to crucify a token scapegoat during a moment of communal outrage-- but doing so rarely addresses the real problem.
As for Microsoft's bottom line, I don't see how it would benefit from Nadella resigning, barring the emergence of a truly significant scandal. As CEO, he's re-energized the company's stock, moved it in new directions in which it can remain a dominant player, enacted a more open dynamic, and generally erased a lot of the ill will that followed the company during the last two years of the Ballmer era. Does Nadella need to show that his apology is sincere? Yes. But is this something for which he should resign? No.