I would try to approach this issue with 2 login entries in 1Password: one login entry with the actual login credentials, and a second login entry with the passphrase. This way you are offered both entries for autofill and you can choose what you want.
In the recent beta/nightly updates, there may be even better support for this approach, because you can define better URL matching. If the web form that asks the encryption password has a distinct and identifyable URL, you can set the 1password entry for the encryption password to autofill on that exact url only, so it is offered only on that URL.
