I have been thinking a lot about doing something similar. While I am not saying to do or not do it, I did want to mention not to jump into this too quickly (unless you're really really sure).
The proverbial can of worms can be opened with this...
1) You'll have to do this for every single cleric character if you want to keep any form of consitancy (this may slow ppl down from choosing the cleric in the future if they think you may yank some spells they really are looking forward to).
2) To be most fair to all players (so that everyone knows what's going on ahead of time) the burden would be upon DM (you) to list out / prepare all the spell lists for all the faiths at the start of the campaign. This way when someone (say 1 month into the game) wants to play a cleric and wants to know about the spell list it would already be available and no "surprises" when they find their favorite spell won't be available.
3) Need to have a firm grasp on balancing mechanics of spell lists (is the spell list for one group "fair" when compared to the spell list of another clerical group)
4) Do you NEED such a system in the rules? If the character is any sort of "good" cleric (per their faith) then they are already going to shy away from the "bad" spells. So (basically what I am trying to say) do you need to do the work to develop something that the players will already inherently do? (again, presumption that the clerics are "good" with respect to their faith, already).
5) And you'd need to be willing to revisit the topic everytime a new supplement comes out with new spells, etc.
And regarding the evil spells, the basic concept already nixes out that option if the character is of opposed alignment (good) so that may be less of an issue for you than you think
now, having said all that, I never was fond of a general clerical spell list for all clerics because I can't some granting access to some of these. I think it also offers distinction between the clerical faiths and a sense of uniquness to your campaign. As said, custom spell lists per faith (and that will probably morph into customer base cleric classes so as to alter skill lists, spell progression, etc) is something I'm still pondering and more than likley do if I ever have the time prior to next campaign. If I don't have time I won't feel it a HUGE loss since #4, above.).