I guess if your system is compromised then password security becomes gravely threatened, no matter how secure the password manager may be. The only partial solution I can think of is to have the OS sandbox every application from every other.
The only ways I can think that would be able to prevent this are:
1. Physical non-networked device password manager
2. Really creative usage of SELinux
3. QubesOS
In all honesty, I could see buying an Android at a Pay as You Go place, and repurpose it to be a offline password manager. Never connect it to wifi, BT, cell. And any APK's you need you load via microSD card and USB.