Sci-fi and a lot of "geekdom" in general does have a misogyny problem.
No, "geekdom" has social-skills issues. A poorly done romantic overture isn't misogyny, it's just another clumsy social interaction. And it doesn't help the kind of people who take things literally that we have so many rules that are taboo to talk about - from "male sexuality is always seen as being dangerous, even if she has more control over the situation than you do" to "people will judge your behavior towards women more harshly".
If your book is about space marines and 90% of the characters are male, that's not misogyny... it's life. If the book were then to only refer to and treat women as sex objects, submissive servants, etc. That's misogyny.
No, that's also (in some cases) life. Or are we banning "The Stepford Wives" now? Or is it just positive or neutral portrayals of those subjects?
Too many people confuse omission for exclusion and both for derision and/or subjugation.
Exactly. Just like some people confuse portrayals or exploration of subjugation with endorsement of it. Or endorsement of ideas that they don't like with evil.
Regardless, you can write good sci-fi in the constraints laid out by the SJW.
You can write good sci-fi without aliens, too. The question should be "Why should fictional entertainment, especially a genre often used as an exploration of ideas, be forced to exclude ideas that one particular group has political issues with?". What's next, communism sucks therefore Star Trek shouldn't be allowed to show a money-free future?