I haven't watched this episode for a while, but when I initially did, I actually liked it for a couple of reasons that do not contribute to finding more sense in the plot flaws you pointed out:
a) I just loved that last scene in the loft. Being on my dark knightie trip, Nick's "If you can't watch, turn away." was just so goosebump-risingly chilly.
b) I just loved it when Nick played moonlight sonata on the piano.
c) I always found that Nick looked particularly ravishing in that flashback.

Now in review I wonder if Lacroix's motive to kill the nun other than upsetting Nick might have to do with the fact that the nun was cheating herself by keeping this box and the money in her possession, which she was not supposed to do. He only promised not to kill the "good sisters" and might argue that she was not "good" in that sense. Far-fetched I know.