Starting a save in 6.5b, and continuing in 6.5c I also had this same thing happening. (6.5d does not seem to touch this part of the code)

Looking into the code with Ctrl + F as well as looking through all of the relevant script and resource files I could find for a while (like princess_persuasion.gd which sets the marry_option flag, among others, and princess_declaration.gd which actually adds Anastasia (and Aire) to your mansion), I could not find anything where the marry-route and non-broken slave-route are treated any different when adding her - both seem to add her in the exact same state in princess_declaration, which is her "standard" state without any changes. Which is in pregen_characters_data.gd, and has her as a slave (and not your wive). I also can't find any timed event fired off there that would start the marriage ceremony later, outside of probably manually marrying her, which seems to have something unique going on in marriage.gd... but doesn't seem it would be any different from enslaving her and then manually marrying her anyways sometime later.

So, either this is intentional and you can no longer get Anastasia as a non-slave (which would really suck, a lot), and the whole enslave/marriage decision and plot would be completely pointless as the outcome is the exact same either way, with her as a slave (who you seem to have no obligation to marry). Or in the current version, her becoming your (non-slave) wive wasn't implemented at all (beyond special text when manually marrying her, as I said).