Two-factor auth appears to break app

[sestaton]

If I set up my ~/.github config file as:

user somename
password somepass
token sometoken

I get the error:

Err: Login with GitHub token is deprecated.

If I comment or remove the token declaration line from the config file, I get:

Err: Must specify two-factor authentication OTP code..

The two-factor authentication is strongly encouraged, so I'm wondering about the rationale behind the 'deprecated' message and also I'd like to know if there is a workaround in this case.