Doing OTP via LDAP/RADIUS isn't really that feasible for what we are looking at. I mean it isn't impossible, but not really something I'd like to pursue.
I would encourage you to consider adding this, if feasible, as it is a nice security feature. A full implementation that integrates with AD and does enterprise certificate authentication would be cool, but that aside just something simple like SSH keys could work well. Just have the ability to add a public certificate for a user and then do a CAPI auth for that. Requires manually updating certificates and so on but gives people the ability to do 2-factor without needing an enterprise PKI setup. Just a Yubikey (or anything like it) and you are good.
The SSH idea is one I may try. It will work fine, Putty-CAC works great with Yubikeys and will give you an SSH key that works properly and requests the right CAPI certificate. So it would work in that card+pin would be needed to access the system. I'll think about that and how much that gets us over just having Webadmin access restricted to a particular set of systems, which require card+pin anyhow.