This guide has now been rewritten and expanded. You can find the new version here.
You've heard right. Fist of the heavens is not that effective against any of the act bosses. The main issue is the speed of casting FoH compared to the large amount of hit points they have. FoH in PvM is mostly as a "launching pad" for holy bolts. Given the amount of undead in the game, it is an effective skill just for shredding bone heads.
You can lock onto Mephisto from the other side of the moat and keep hammering him with it, just expect to be drinking a few mana potions before he falls over for you. It is also a good trick to flush diablo out. He doesn't like being hit from out of range of his lightning hose so if you FoH him from afar, he will usually charge you, for better or worse.
Jewels of lightning or thunder are fairly common. They get pricey the better the damage. You can get up to 1-100 lightning damage on them which is better than what topaz's can offer.
Lightning immunes or any elemental immunes aren't a problem as your eletemplar should still be doing fire/cold/lightning/physical damage from his zeal. Lightning immunes are only a problem versus fist of the heavens. Most lightning immunes when convicted will still offer a good amount of lightning resistance making fist of the heavens quite weak, so usually lightning immunes are best dealt with using zeal.