eDirectory is independent of the protocol running on the servers. Obviously the servers need to be able to communicate for eDirectory to function, but it doesn't matter what protocol is used.
If you want a pure IP environment then you either need to allow all multicast traffic through your routers or setup SLP. SLP is very easy to configure and the default works great. If you have a large tree and network you may want to configure SLP so that you have more control over it, but the default will work fine.
The clients will have to be reconfigured as well so that they know the IP address of the DA as well as the name of the scope that is hosted on the DA.