The main advantage comes in the ease of production due to upgrade paths. One temple of Lunord lets you convert as many Cutthroats as you want into Assassins. Training a Rogue, then upgrading it twice, results in you paying 800 for a unit that would otherwise cost 700 and which can be built practically anywhere in only two turns. Even if the Monsters or Undead get a variety of temples up, you're still stuck with training your Paladins of Life at the city with a temple to Agrela or upgrading your Court Werewolves, paying 1300 to produce the unit in whichever town you have that can produce Court Werewolves. If you scrimp on infrastructure and just build Noble Werewolves and upgrade them twice, you can train them in more towns but end up paying 1495 gold and taking four turns to train them. Humans can do this for a lot less money, and have a lot easier time generating the cash necessary to use this strategy on a large scale.
Actually the Ratman line upgrades to Paladins of Life and works pretty much the same way as the Rogue->Assassin line (cheap, hired by gold income buildings), and the Goblin Archer line upgrades into Champions of Grum-Gog. Werewolves are expensive yes, they are also ridiculously powerful.
The Healer hate is because they are bad. Really, that's it. They cost too much for what they do. For the cost of three Healers (1500) you could get two temple units (700 each) and stick a couple of upgrades on them. Or if you want to compare them to lower end units, a single Healer costs you as much as three Rangers with Silver Weapon upgrades, or three Mages. Even upgrading them to Priestesses of Agrela isn't a very good move, since you pay 500 for the Healer and then another 700 on top of that to upgrade them. The good upgrade paths start with cheap units and then convert to expensive ones so you only pay a small premium over the normal cost of the expensive unit, but Healers to Priestesses is expensive to start with, so you pay a 500 gold premium every time you upgrade. The infrastructure to build Clerics isn't very common anyway, and Healers are even harder to build, so in addition to being exorbitantly expensive your production capabilities of these units is still going to be quite low.
I'm not really sure how 500 is a lot, considering it costs like 1500 to perk out most units anyway, and ideally you aren't building lots of units, you are building a few, perking them out and buffing them as fast as possible, then wrecking things with them. With humans I can't spend my gold fast enough anyway.
I think you're drastically overstating the typical level of resistances to other damage types. The majority of units don't even have armor at all, and six of the fourteen Monster units take bonus damage from Missile attacks. Fire Elementals have less than 75% reduction from physical attacks of all kinds, and they are the only thing I can think of that gets even that high. Gold Dragons have somewhere in the vicinity of 55% damage reduction against missiles, and they're definitely more resistant than most enemies you'll face. Once you add Silver Weapons for a 20% Spirit damage bonus on all of your Fighter and Ranged type units, the moderate Spirit damage done by Healers really doesn't stack up well.
There are very few enemies that are highly resistant to both physical and elemental attacks. If you have a mix of decent units you can kill enemies by exploiting their resistance holes with higher damage units, rather than using a more expensive, lower damage unit that works on everything. There's nothing a Healer can kill that you couldn't kill with two Mages and an upgraded Veteran.
Are you playing on impossible? Every single enemy unit by mid-game is loaded with perks and sometimes buffs, with temple units in their ranks that have ridiculous resists just like your own. A fully buffed up unit (+100 death damage, +75% elemental, +50% life) with a few +20% perks from leveling and whatever weapon perks you can get, still can't kill many of these units that quickly. A couple healers can. It really is that impressive.
Besides that, the most common powerful units type in the game happen to be highly resistant to physical and elemental attacks, as well as being immune to death damage... elementals. Clerics in small groups can start taking out greater fire elementals very early in the game giving you early access to temple sites. Without chaos shield and jewelry very few mid game melee units can even approach a greater fire elemental, and any missile or elemental ranged unit is just going to plink at it for nominal damage. Clerics will hit them for full damage, four of them can kill one before it can retaliate. 2000 gold for a temple site on turn 30 is well worth it, and they continue to excel in doing damage to otherwise highly resistant units throughout the game.
I would go so far as to say Priestesses of Agrella are the best units in the game, with Ordained Shaman and Healers right behind. Spirit damage really is that important when playing late game on impossible (and eventually multiplayer). The only other thing that comes close to comparing are units with ranged AoEs, like Champions of Grum-Gog and Court Werewolves (not Helias), followed by Liches and Paladins of Dauros since they are totally ineffective against certain races.