Either you can do it from config.xml file, but bit risky.
Apart from deleting the managed server from config.xml which might be a little bit risky so the other option is to delete it from Console .
So please login in to the Weblogic Admin Console using the the URL http://<host Name on which Admin Server>:<Admin Server Listen Port>/console
Once logged into the console please follow the below steps in order to delete the Managed Server :-
Goto -----> Environment ---> Servers ----> Click on Lock & Edit in the change centre ------> Then Select the Managed Server which needs to be deleted -----> Click on delete -----> Activate the changes in the change center.
Since you already configured webcenter spaces managed server for that domain(which you might have deleted now) , you cannot configure the same managed server again for that same domain ( I guess you might have choosen to extend domain).
Other option is to run the config again and create a new domain with new webcenter spaces server .
Alternate option which might work or not -- Run the config again and choose expand cluster for the existing domain and check if the webcenter spaces is enabled or not. This option will be enabled only if you would have choosen "Clustered" option during the first run of the confiig.sh
1. Login to weblogic console
2. Down the managed server
3. click on lock and edit if enabled
4. select the managed server and delete it