I believe you are alright. If you defeat the church boys Anri will show up in firelink, then in the catacombs location A, then location B. This is true whether Wolnir has been defeated or not.
I'm also fairly sure that even if you miss this entirely, Anri still gets assassinated at the temple if you don't kill the assassin. It's difficult to completely foil this questline as long as you remember to get your 5 darksigns before Abyss Watchers.