I have the same problem. I do not want to restart my mac because I work on it and it takes some time to arrange all windows and desktops after a restart. Additionally I cannot keep the external backup drive connected all the time, because I have other devices that I need to attach and there is not enough ports for all of them. I tried to create an encrypted partition, then use it as a backup, but time machine reformats it as unencrypted, then goes on creating encrypted backup.
So I wiped out the partition again and set it up for Time Machine turning off automatic backup. I left it working overnight. Even though, the drive is essentially empty, there is no single backup yet, it still shows "Encrypting..." after more than ten hours with almost no progress:

Now I see it made a little progress, but I think it will take a few weeks to encrypt the entire drive. This is insane!