Pavel,
I have always been able to stop citadel services on my achine by using lkcitdl.exe -stop. I couldn't pinpoint a reason why you could be gettiing this error. But one thing of interest would be to know your version of NI Logos. If you have a version of NI Logos older than 4.4.0.12, I would encourage you to unistall the old version of logos and install logos 4.4.0.12 from http://digital.ni.com/softlib.nsf/954feaeea92d90918625674b00658b83/c1a484551a75614686256ae300734336?OpenDocument
With this i think you should be able to stop Citadel services programmatically.
Hope this helps,
Pravin