How about divine feats instead of domain powers? Clerics of different deities are essentially different classes unto themselves. I realize this would be straying from the core 3.5 rules probably too far, but it would make for a more diverse set of characters. For that matter, why should all clerics turn/rebuke undead? At first level, you could just pick a divine feat. The overall class ability could be called "channel positive/negative energy", or something like that.
As for the domain powers, they're pretty good. My biggest complaint as a cleric was having to spend three rounds ramping up in a fight just so
I could make a decent attack. But you can't do that because everyone else is getting pounded on and needs to be healed. What's the point of align weapon if you never get to cast it? So for a domain power, how about certain abilities always being active? The good domain second level power align weapon could be "pick a weapon, it's always aligned". You could perform a ceremony to align it taking 24 hours or something. There might be a balance issue, but I can't see it. Just a thought.