Yes.  It is not a recommended practice to allow anything aggressive to continue to remain resident in memory longer than necessary.  However, you can go to the blue “IT” icon in the system tray and right click on the program and choose “End Program” from the list.  This will end the messages box from returning when you close it.  Repelit will continue to protect you.  The warnings, notifications and install modes will be offline.  The blue “IT” logo will return to the system tray when you restart your computer and Repelit will be running normally. 

After running your system with an aggressive piece of Malware running in the background make sure you leave your log on screen up for a few minutes before signing on.  This will ensure Repelit has enough CPU resources and time to remove any Badware (if there is any) on your system.