Think about things in reverse...
How can the god of death and desctruction appear to be a champion of good and holiness? Not just have the occasional benefit, mind you, but truly Good For All? What's the benefit of it? Why do those who worship it think of it as a good thing?
How can the god of light and purity seem wicked and deadly? What would be things that the good church would cover up?
One way to go about this may be to have a lot of high-ups with rings of mind sheidling and such.
...and just because the god is evil doesn't (nessecarily) mean all followers are. Those alignment restrictions are for clerics only...the day-to-day operators of the church and believers in the faith don't have to be evil.
Heck, I could think of a situation where the cleric wouldn't have to be evil, by nessecity. If they were interested in appeasing the god of death and destruction, or in the nessecity and beauty of things being cleared away to make room for the new.
Basically, IMHO and IMC, actions themselves aren't evil. It doesn't so much matter that you kill and eat babies as it matters *why* you would do such a thing and how you would ract to such a thing.
It's like...say we take a Mesoamerican/South American-style pantheon. The gods here *require* human sacrifice to live, to gain power, and to help out the human race.
In your typical D&D campaign, any cleric sacrificing people is a flagstone for EVIL!
But it could be that the only reason the sun rises in the morning (and, hence, plants grow and life continues) is because someone is killed to feed the sun.
This is definately a Lawful situation (needs of the many vs. needs of the few), but it is, in fact, a good act. Offering yourself up for sacrifice is a holy thing, and, when no willing candidates are found, you may have to do it do those who don't want it...but still, if you don't, you doom humanity to darkness and suffering, so you've *gotta.* You may not take pleasure in it, but it is an act of goodness, if you do it with the motive of helping out the entire world.
Similarly, most Good churches are associated with healing and recovery...but it could instead be associated with pestilence, starvation, and suffering. Life becomes a curse that death is a freedom from. Most people seek to end their existence, but a priesthood wishes to keep them down. Their motive is nothing more complex than greed and gratification...they hold these people back, infect them, they don't get infected themselves. You've got healing and recovery, all unwilling. Cure Disease looses it's relief powers if the disease just returns stronger than before.
Basically, if you want to blur the line, think about what it would take to have Evil and Corruption be regarded as a benefit -- why would it be good? Think about why Good and Purity could be very bad things....why would those who support the Dark Church rival the Pure Church, then?
Answer a few of these, and either make potions of glibness/rings of mind shielding/whatnot be available, or ditch the detect alignment spells.
IMHO, of course.
