When you install or remove mongod as a service, the standard shutdown sequence occurs as if mongod actually ran. Illustrated below.

It should be ensured that mongod is not actually starting up, and then remove the calls to the mongod shutdown sequence.

D:\justin's projects\mongo>db\Debug\mongod --remove
warning: some regex utf8 things will not work. pcre build doesn't have --enable-unicode-properties
Fri Jun 11 16:50:29 dbexit:
Fri Jun 11 16:50:29 shutdown: going to close listening sockets...
Fri Jun 11 16:50:29 shutdown: going to flush oplog...
Fri Jun 11 16:50:29 shutdown: going to close sockets...
Fri Jun 11 16:50:29 shutdown: waiting for fs preallocator...
Fri Jun 11 16:50:29 shutdown: closing all files...
Fri Jun 11 16:50:29 closeAllFiles() finished
8 mutexes in program
exit
LastErrorHolder
getNonce
BackgroundJob
rw:mmmutex
Logstream
Ports
ListeningSockets
Fri Jun 11 16:50:29 dbexit: really exiting now

D:\justin's projects\mongo>db\Debug\mongod --install
warning: some regex utf8 things will not work. pcre build doesn't have --enable-unicode-properties
Fri Jun 11 16:50:35 dbexit:
Fri Jun 11 16:50:35 shutdown: going to close listening sockets...
Fri Jun 11 16:50:35 shutdown: going to flush oplog...
Fri Jun 11 16:50:35 shutdown: going to close sockets...
Fri Jun 11 16:50:35 shutdown: waiting for fs preallocator...
Fri Jun 11 16:50:35 shutdown: closing all files...
Fri Jun 11 16:50:35 closeAllFiles() finished
8 mutexes in program
exit
LastErrorHolder
getNonce
BackgroundJob
rw:mmmutex
Logstream
Ports
ListeningSockets
Fri Jun 11 16:50:35 dbexit: really exiting now