Acho que você está limitado a alterá-lo no arquivo de configuração do upstart, assim:
# Ubuntu upstart file at /etc/init/mongodb.conf
limit nofile 20000 20000
kill timeout 300 # wait 300s between SIGTERM and SIGKILL.
pre-start script
mkdir -p /var/lib/mongodb/
mkdir -p /var/log/mongodb/
end script
start on runlevel [2345]
stop on runlevel [06]
script
ENABLE_MONGODB="yes"
if [ -f /etc/default/mongodb ]; then . /etc/default/mongodb; fi
if [ "x$ENABLE_MONGODB" = "xyes" ]; then exec start-stop-daemon --start --quiet --chuid mongodb --exec /usr/bin/mongod -- --config /etc/my-mongodb.conf; fi
end script
Acima, alterei o caminho nesta linha:
if [ "x$ENABLE_MONGODB" = "xyes" ]; then exec start-stop-daemon \
--start --quiet --chuid mongodb --exec /usr/bin/mongod -- \
--config /etc/my-mongodb.conf; fi