If we have dangerous cults we'll also need a new "priest/inquisitor" noble. If there are "unacceptable" cults that cause havoc, they should be countered with beneficial cults that help your dwarves. At the very least we'd need a way to root out and stop the influence of negative worship. So we can appoint a high priest and/or inquisitor and then designate a shrine for them. It would be a room with an altar (I imagine all dwarf altars to be anvils covered in either booze or hippie blood) or two and several statues. The statues would be either of hte deity itself or activities/items it approves of. So for a war god an "Iron statue of Urist McGorefist striking down a troll, it menaces with steel spikes" would count (probably triple). The altar could require gems or other rare/materials preferred by the Deity in question. The priest would help recruit for the "proper" cult and perhaps work on bonuses related to it while the inquisitor would root out heretics. Once he's identified heretics, you can send in your hammerdwarves to lay the smack down/arrest/torture them.
I imagine your official religion being able to boost the craftdorfship of your fort. Either a passive learning speed increase or a way to (temporarily) let worshipers craft at a higher level. It would be like making a preferred item, except you'd be became a preferred religious item. So a dwarf that likes steel who worships a hammer loving diety would be your ideal weaponsmith... so long as you appease that deity. Other bonuses could be quicker crop growth times, advance warning on sieges, removing invisibility from thieves/ambushers, allowing your priest to divine/scry the location of gems and precious metals, combat bonuses against hippies, and so on. The # of worshipers and the (perceived) value of their shrine/temple would influence how many booms the deity in question grants you.
For this to be truly fleshed out, I'd love for hte player to appoint an "official" religion of the fortress. Then you can choose to ban all other cults, or set up a list of "approved" religions. Then you can choose to go "darkside" and become a necromatic fortress. You can have vampire champions and a moshpit of zombies guarding your door. Obviously this would piss off the mountainhome and all your neighbours... so you'd need all those vampires and zombies to fend off the constant sieges! Just think of the FUN! Having to fight off squads of legendary hammerdorfs clad in steel with your army of troll thralls lead by your vampire champion! BONUS! Evil shrines could make use of all those useless blood/ichor barrels that caravans bring. Thus you could give blood to the blood god, and receive his blessing!
Again though, at the very least if we have evil dwarves secretly murdering people in our forts, we need some way of actively rooting them out. Something like an inquisitor (or several, as I imagine s/he'd be #1 on the cultist murder list). Keeping your dwarves happy should also help fight cult recruitment. Your shrine would give bonuses to the fort, and having a grand temple to your civilizations chosen deity could be a requirement to draw the monarch to your fort. Individual nobles could also request private shrines, then get pissy that the mayor or a lesser noble has a better one. Then you could persuade that noble to pull a lever that drops him 100z levels to decorate the walls of your new temple set above magma sea. PRAISE ARMOK!