Okay, but the attacker has RCE on the system doing the decryption, so they can scrape the encryption keys or the vault data out of memory. This appears to be a APT, probably a State-level actor. Once the production work machine was compromised, it's all over.
I'm not aware of any 2FA that could be successfully integrated into a symmetric-key encryption algorithm. How do we fix 2FA without making the entire password vault system dependent on network access to a central LP server that is not compromised?