Move parameter logic from altering init conf file to the /etc/mongodb.conf file. The mongdob service is already configured to read parameters from the /etc/mongodb.conf file and moving the configuration options inside the config file allows the systemd style service to start properly.
Also, as of MongoDB 2.6, the specification of master/slave flags on startup is not allowed to be specified with the replicaset flags. This change allows for the master/slave flag to be specified in the /etc/mongodb.conf file only when the replica-set (peer) relation has not been established. Prior to versions of MongoDB 2.6, specifying the master/slave flag on startup did not cause MongoDB to error out and MongoDB ignored the flag.