I agree with Romeo Steven's comment that the issues seem orthogonal. As an example, (caveat YMMV), Steve Sailer believes in HBD. However, he frequently cites lower growth in african american wages as a reason to shut the american borders down to low skilled workers.
However, in today's environment, I'm not sure how many top-rated charities are HBD believing. A neoreactionary charity aiming at improving Africa might do many things differently. And being a relatively new ideology, most policies would not have substantial support of data. Hence, atleast in the current scenario, you would not find many people that were HBD aware and contributed greatly to african charities. However, it is not intellectually inconsistent.
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.