I think you are covering a lot of distance by stretching "don't advocate violence" into "don't say anything that someone feels the widespread adoption of could be potentially dangerous."
Actually, this is something I've been a bit confused about the whole time. What posts is she talking about? The OP says Yvain's posts, but from the substance of the article the article it sounds like she's talking about reactionaries.
Considering the much higher than average rate of homocide towards trans people based on todays standards, a reinforcement of gender roles would almost certainly increase that rate.
A long blog post explains why the author, a feminist, is not comfortable with the rationalist community despite thinking it is "super cool and interesting". It's directed specifically at Yvain, but it's probably general enough to be of some interest here.
http://apophemi.wordpress.com/2014/01/04/why-im-not-on-the-rationalist-masterlist/
I'm not sure if I can summarize this fairly but the main thrust seems to be that we are overly willing to entertain offensive/taboo/hurtful ideas and this drives off many types of people. Here's a quote:
The author perceives a link between LW type open discourse and danger to minority groups. I'm not sure whether that's true or not. Take race. Many LWers are willing to entertain ideas about the existence and possible importance of average group differences in psychological traits. So, maybe LWers are racists. But they're racists who continually obsess over optimizing their philanthropic contributions to African charities. So, maybe not racists in a dangerous way?
An overly rosy view, perhaps, and I don't want to deny the reality of the blogger's experience. Clearly, the person is intelligent and attracted to some aspects of LW discourse while turned off by other aspects.