I like the idea of using Wis instead of Str or Dex with the deity's favored weapon in that it provides a way for a cleric to be immediately proficient in combat without casting a half a dozen spells. The feat to which Windblade is referring to only applies to simple and natural weapons, so Falan, Stasis, Dedestroyt would never use it. I think it makes sense that as part of clerical training you would focus on the use of the favored weapon, and in some instances (Tyrogatore) it is a major part of religious practice. However, as Windblade pointed out, it is a little vanilla. Practical, but vanilla.
If you don't like that idea, how about something similar to the death domain's death touch ability? 1/day invoke the ability, roll to hit. If successful roll 1d6 per cleric level, if you exceed the target's hit points, it dies.