I don't think it's any surprise that a white man living in the 1800s would have such outdated ideas about race and sex, or that such notions would show up in his work. This is pretty much the history of mankind. As we progress, we can strip away the bad ideas and test what remains. Indeed, you can remove such content from Darwin's work and still have the early foundation for what is known today about evolution.
It is more than 150 years now, since his book was published. Much of his work has been expanded and built upon, and some has been replaced as more knowledge was gained. The consensus amongst scientists today is that there is no question that evolution explains the diversity of life, and that it is a normal part of biological life. There are differences, to be sure, but these are similar to the differences in any of the sciences- at the leading edge of discovery and understanding, competing hypotheses are being put to the test.
That is the essence of the scientific method- show your work, and keep pushing forward. Today's questions become tomorrow's answers. Some of what is hypothesized today will be discarded as we learn more. Those who feel that it is wrong are free to challenge any part of evolution. But if you can't show your work, you won't get far.