OMPI doesn't do anything relative to the .ssh directory, or what key is used for ssh authentication.

Afraid that is one you have to solve at the system level :-/
^ In that case, where and how does OMPI call ssh? 

ssh has a '-i' option which can be used to specify the id_rsa file.  If ssh is called in a script (or if there's a way to pass ssh args into OMPI), then I can just use that ssh option.