In order to satisfy the CM perquisite check, the site server must have at east the WSUS service installed, which I have.
That just doesn't sound right. It's certainly not a requirement for CM2012R2 or previous.
Are you seeing this in CM Current Branch (1511 or 1512) ?
The site server has no functional requirement for WSUS at all in any way. The SUP sure does. IF you have installed the SUP role on your site server, then it's actually the SUP role which requires it, and the binaries/console etc are certainly required, so
that the SUP component can make the relevant API calls to the WSUS services.
If you do launch the post-install-config task (which you can do so), you can proceed up to a point, which would satisfy the nag-box, without compromising your design.
Don [doesn't work for MSFT, and they're probably glad about that ;]