The thing to remember about the Turn ability is that it gives you access to all the feats that use the turn charges. That was one of my major complaints about the original altered domain powers/changes to the clerics that were made when we switched to 3.0. If you take that flexible ability away and replace it with something like water breathing I think the cleric gets de-powered.
I am a very confused by your comment. The turn ability granted to the clerics of Lakius is the ability to cast water breathing spells. Which also can be used to power the divine feats so they basically trade out turn undead to breath water and they can still use the water breathing to power divine feats. That is DM's call but seems ok to me.
What I am talking about here is the water domain ability which is:
Turn or destroy fire creatures as a good cleric turns undead. Rebuke, command, or bolster water creatures as an evil cleric rebukes undead. Use these abilities a total number of times per day equal to 3 + your Charisma modifier. This granted power is a supernatural ability.
I don't like that for a domain ability. This domain ability has nothing to do with the turn undead that clerics gets or water breathing that lakius gets.
That being said I would like to think of another ability for the domain ability for water. If we do that then we will likely have to do the same for earth, fire, and air. Just checking to see what everyone thinks.