Yeah. Even with this mod installed, you can still kill him. It just gives you an option.
I Have been testing these mods pretty extensively. I just started my second playthrough on Anatriax's setup. Last character completed Main Quest, Civil War (Imperial), Dragonborn, and Dawnguard questlines, along with quite a few smaller quests. 40+ hours without a single CTD, hang, or problem. Current Character is a magic oriented character. I will be doing Dawnguard, Mages Collage, Dark Brotherhood, Thieves Guild, Main, and Civil War (Storm Cloak). 10 hours in, and I haven't had any problems yet.