I thought "The War Prayer" was an ok episode -- not great, but not sucky either.
There are some moments I really, really like though. For example, I loved the scene in the medlab where Londo tells Shaal Mayan that Aria and Kiron will get over wanting love, and Shaal Mayan replies to Londo, "Just as you did." It's a striking character moment for me. Shaal Mayan felt a wee bit bland for much of the episode, but this moment for her and Londo was superb.
The bringing of Human hostility toward aliens is of course seemingly decent on being somewhat stand-alone, but it is great in setting up for the movement of some Humans in the future of the show to become aggressively isolationistic.
I liked the introduction of the Abbai and personally wish they were a background alien that hadn't been abandoned; I thought they looked rather interesting and that they had potential to pop up here and there and would have looked nice as one of the more prominent lesser races in the coalition against the Shadows.