Sorry for the late answer. In order to try to find the solution about your question, we took time to analyze with development team of mongobird.
In conclusion, there is no way to communicate directly with mongod with the keyfile except mongos because of the security policy of MongoDB. Therefore, you will not be able to connect to mongod with the keyfile through mongobird. Your question occurs even MMS of 10gen. Refer to the following site.
https://groups.google.com/forum/#!topic/10gen-mms/NGTQotYLzw4
If you want to connect a mongod in mongobird, you must register the mongod to mongobird after created the administrator account of mongod individual. It supports kerberos authentication from version 2.4 of mongodb, but this is only supported on mongodb enterprise version.