If I could sneak the comment in, you're likely to have this problem with all of the primary casting classes, and with untweakable classes (like the Red Dragon Disciple, which would require haks to alter), due to the way that certain classes (read: paladins, fighters, barbarians, rogues, rangers, monks) rely heavily on gear and the way that others (read: bards, clerics, druids, wizards, sorcerers) do pretty well regardless of gear.
If the goal is to balance casting classes (clerics, in particular, take the day when only mundane kits are available) to the quintessential paladin/(ubered) PDK of the concept, you're liable to end up with a massive project. I would ask for an approach more the route of "encouraging specialization," than of "balancing the classes." With the cleric example: we're looking at a class that's, in its conceptual essence, a support class, but they dominate in the melee thanks to buffs that focus on durability (on a server where challenges are primarily swarms of bad guys, so buffs that a paladin, for example, would have - which are great for dealing damage but useless on the defensive - aren't nearly as effective).
Anyhow, to the actual suggestion: I think the most effective way to put clerics on the support role instead of the tanking role is to make their DR-producing spells less effective on themselves, but just as effective as normal when cast on others, to make magic vestment not work on shields (as targeting other people's shields is a bit of a pain in the arse, and the shield bonus is thus generally used on oneself), to make aid give out more HP (1d4 per 2 caster levels? would avg 25 temporary hit points at level 20) to others, to put a bonus on the effects produced by endurance when the target has a certain number of levels (10?) in a martial class, and to (possibly) make healing items harder to come by (but that last one is a risky idea. If you can make people party up, that would force the clerics to spend their spell slots on healing, but that's a mighty slap in the face to the soloer.) After all, there's no PvP on the server; no sense in fussing over which PC can kill which other PC. 'cuz they won't. Trick is gonna be getting people to play and have fun without killing nearby people's fun. (and having the non-fighters be better fighters than the fightin' classes definately steals thunder.)