1. Can you kill them?
2. Do they play a major part in your world?
3. Do you just hand wave them away except for letting the cleric have access to divine magic?
4. Do your good temples all get along is the only strife if there is any between good and evil churches?
5. Do you require your clerics to tithe to their churches?
6. Do the cleric gods every get angry with the cleric and block access to his spells?
1. Possibly, but very difficult, it would be the culmination of an epic quest to weaken a god, discover and exploit his vulnerabilities, gain allies and sufficient personal power to do the deed. Failing or abandoning the quest would be quite likely. Success would probably involve one of the party having to take the place of the deceased god, in some capacity. Since the endgame would be the end of the campaign this would be possible. (Quasi-deities and weaker demigods are much easier to kill, though still likely an epic task.) Gods have an alarming tendency to come back from the dead, though...
2. Yes, but this is coloured by the attitudes of the players. A lot of players don't care or actively avoid fantasy religion, and pushing it down their throats is as counterproductive as it is in the real world. To those players who are interested there is plenty to become involved with as regards religious institutions, holy places etc.
3. As I said above, some players aren't interested. Generally, I require players of divinely powered PCs to be somewhat interested, and not using their "religious" PCs solely as parodies or criticism of organised religion. I would probably allow a "just the powers" cleric in a dungeon crawl game lacking social context.
4. In my campaigns there is plenty of competition between religions of all kinds, but it's less likely to get seriously violent between good religions. I do run a fairly black and white world, with plenty of aggressively evil organisations and religions, giving plenty of reasons for non-evil faiths to try and get along despite their differences. And I really hate the tendency in some games to turn LG churches and paladins into evil, intolerant fascists while remaining LG.
5. It depends on the church. Lawfulish faiths tend to have a formal tithe or similar. Less organised religions may lack the internal civil service to collect a formal tax, especially if they don't have temples, but their clergy generally make charitable donations or sponsor related activities.
6. As a DM I'm much less willing to do this nowadays than in previous years or editions. Unless the player wants to go through a crisis of faith, this generally denotes a lack of communication between the DM and player or differing expectations, in which case punishing the player is likely to aggravate matters further. I find its crucial that the players of PCs with strong institutional or religious connections have a well-defined ethos and clear and unambiguous expectations from the game. I've seen too many car wrecks from assumption clashes to take this subject lightly.
I prefer the 4e approach where heretics keep their spells, but have to deal with the social consequences, with church hit squads and maybe angry angels. This keeps the PC a viable adventurer while providing adventure hooks, and allowing for non-suicidal heresy. Now the spells of heretics may change in appearance in an involuntary way to reflect the changing faith of their source, and heretics who diverge greatly are more likely to move to another religion closer to their new tenets.
