Windows – Remove active directory certificate service role – Windows Server 2008 R2

AD DS is a server role that can be removed just like any other server role. Run DCPROMO on both DC's to demote them. When you demote the last DC make sure to select the option that it is the last DC in the domain. This will revert both DC's to standalone servers.

You're probably going to need to revisit and probably reconfigure DHCP and DNS in order to continue to serve your network clients.

EDIT:

Here's my opinion on some of the issues you related in your comment:

rDNS zone missing: an rDNS zone isn't a requirement for AD. It's a preference. There isn't any function of AD that needs or requires an rDNS zone. I personally prefer to create an rDNS zone.

AD Recycle Bin not enabled: Again, this is a preference and not a requirement. I prefer to enable it.

IPv6 enabled: This is debatable. I'm not convinced that it should be disabled. I know that there's a lot of information on the internet for and against but I've never had an issue leaving it enabled and I haven't seen any technical information from MS that recommends disabling it.

No Replication: If the DC's aren't replicating than that's definitely a problem that would need to be resolved if you were leaving the domain intact.

I'm not sure why @whizkid thinks Microsoft doesn't recommend in-place upgrades. That might have been the case way back in the 2000/2003 era of Windows. But ever since the Win7/2008R2 generation of Windows, in-place upgrades have been pretty well supported. In fact, it has basically become the new default for desktop OSes. Just look in the tech news for all of the annoyed reports from people getting auto-upgraded from Win7/8/8.1 to Win10.

I've personally performed a decent number (10+) of in-place upgrades from 2008 R2 to 2012 R2 on domain controllers in production environments without any issues whatsoever (aside from the expected downtime during the upgrade process). Admittedly, most of those were running nothing but DC related services. But in any case, I wouldn't let the fact that the machine is DC stop you from attempting an in-place upgrade. But as always, have backups just in case.