I think your best bet for this flavor build is to skip cleric entirely ( just role play), get 1 rogue level so you get full skills in stealth and stuff, build for intelligence and stamina with a bit dex, then take the next 4 levels as alchemist (or every other level 'til you have 4 alch) get batallion brew for int bonus to to hit and damage, the apothecary tree gets you some healing and your stealth will not be super bad.
Another path would be to go Dark Hunter all the way, you will have stealth, some healing and assassinate abilities, this is probably the strongest option for a new player. You just have to lie a bit about being clergy, not a big deal, look at the real world for examples