malicious and accidental deletions
If a malicious hacker deliberately destroyed data, they would have to know about CloudBerry and where the backups were stored. Makes me think this was someone known. You can secure the agent with a master password - that feature is used to prevent end-users from using the agent. This feature can be automated from the console using the RMM - Remote Deploy - Create Configuration option. Create configurations for Windows and Mac/Linux and enable the Protect Console with Master Password option. Then create a rule for each config that deploys the settings to all customers (or a subset as needed).
The rest, I think, is security related like not storing passwords in web browsers to prevent someone from logging into the cloud storage vendor via a web browser, disabling credentials as a part of the process when employees / consultants leave, changing any shared passwords if you use them, etc.
You can also enable IP Address White Lists in the console to prevent unauthorized access via the web console from unknown IP Addresses.
And lastly, notify the authorities. If it was someone close, they can probably find out who.