Little Snitch & co aren't anti-malware solutions even if they seem like they might work against that. Anything which is running on a malware-infected system can't be trusted.

Such firewalls are used for protection against asshole developers which want to collect analytics without asking for confirmation. Apple are one of the assholes and LS can only be an interim solution against the OS developer. This was bound to happen... and I guess only a HW solution will help now.