OpenVAS is free, but the big issue we've had with it is the complexity of setting it up and maintaining it. We are a security team, and would rather not spend our time managing servers, especially since we aren't the best people to do that at Cloudflare.
Shameless plug: I got it to work. Will be doing a talk about the experience at week's DC4420 meeting.
I've looked at it (openvas), got something working, but was never happy with it and ended up returning to a simpler/proven nmap base that I could manage better and add complexity if/when needed.
On the other hand.. I do have something that might be enough to get you going. The setup we built is open: https://github.com/smarkets/vuln-scanner - go have a look.
The glue code has comments on some of the stranger bugs I had to work around. So does the readme. If something isn't clear, feel free to ask.
One of my challanges was understanding the the zoo of tests OpenVAS would run and trying to reliably select which ones to apply. Did you, or anyone here, ever spot a way of outputting all the tests (nmap scripts etc.) that a particular run would trigger (but without actually running them)
I think there might be a way to choose categories to include/exclude but haven't had the time to actually investigate.