Hi devnull thanks for the motivation…
I tried implementing it using ‘psexec’ but it did not work out as expected. anyway I found out why my service was not terminating when called from webMethods. That was because when the service calls the command ‘psexec’ the service should in return accept the EULA of the program PSTools, but webMethods doesn’t know how to accept the EULA. So I went thru some microsoft forums and found out a switch to be added to the command to accept the EULA, so now the command becomes…
psexec -accepteula \machine1 -w F:\IntegrationServer F:\IntegrationServer\packages\napster\cmdexe.bat
But somehow even this did not work out as expected. So gave up on this approach.
My second approach was simple and effective. I just mapped the shared drive from remote system to my local machine using the command ‘net use’ from webMethods(which is on local machine). Now I ran the command on the mapped drive to get what I wanted. 
The ‘psexec’ command works like a charm when used from my local machine without involving webMethods!!
#Integration-Server-and-ESB#webMethods#Flow-and-Java-services