Euphie is adopted into the royal family; 'stepsister' isn't the right word for that, but maybe bad word choice, or bad translation. The LN translation also uses 'stepsister' at this point.
I don't think "axed" is the right word; the manga reached a natural arc conclusion, same as the anime. Much better stopping point than the WataOshi anime, say. And the manga made a surprising number of changes vs. the LN, like giving Tilty a bigger role, and changing the big climax battle. I think Lumi might have more to do as well, don't recall her protecting the audience.
The manga ending was kind of weak; in the novel, they're exchanging "off to work" kisses in the morning. (Like at the end of episode 12.) That said, be reminded that in manga chapter 50 they did kiss, and in 51 Euphie basically claimed Anis openly. It's still yuri.
What's in the LN? Lots more details, different POVs, and, after this, even more yuri. Also after this, more politics, visiting her brother again, resolution to the lifespan differences, and more!