Resolution:
Yes, there is a way to disable the confirmation prompt while running the script.

For example, if you create an admin script  called admin.sct with commands to delete queue, it will ask the user for the confirmation to delete the queue before deleting when we run the script as  
"tibemsadmin -script admin.scr" with the username and password to connect.

If we want to disable the confirmation, you can use the option -ignore like

"tibemsadmin -script admin.scr -ignore" to disable the confirmation. Now, this won't ask the user to confirm and it will go and delete the queue without asking the confirmation.