In order to still be able to work, I've opened XCode-Preferences-Source Control and unchecked "Enable Source Control". They didn't bother adding the UI controls to allow you to bypass the validity check for a SVN certificate.
Connect once using command line tools and accept server certificate permanently.
I am having trouble connecting my project repository to XCode, ever since I've upgraded to 4.2.
I have a local server with a forwarded port to be accessed from outside the local network. When I explicitly define the external ip (i.e https://123.456.789.000/svn/...) the repository is properly linked, no problems.
This also works when I specify the internal address.
For more information, and the place I found my answer, please refer to this answer.