I have the free version also, and kept getting this message all the time too. Very annoying.
I found that after you run a scan, with the free version, you can go into the system tray, enter on Malware Bites and arrow down to the ‘quit Malware Bites’ option and enter on it. This will remove it from the system tray temporarily and the announcement will not come up again until you run another scan.
You will have to go through these steps after every time you run a scan manually.
I only run a scan about once a week, so not a big deal to go into the system tray and do this.
I don’t think it would work with the paid version, as it is always running with real time protection.