Hmm, looking at "Add Alternate Mother / Father", it seems that the default relationship type when you add a parent to your tree is "biological" but you can change it to one of the following:
adopted, step, foster, related, guardian, private, unknown.
So it looks as though what I need to do is change her legal father to one of those ("step", I guess is the nearest) and add the other as "biological". But I'm not sure any of those categories really fits the bill properly.