I've played and won with the Elohim without ever taking an enemy city - so it was like I didn't even have the Tolerant trait. I found them quite powerful without that trait.
Spiritual is a very powerful trait, imo, because there is a lot of incentive to cycle through multiple religions over the course of a game. For example, you might use RoK to boost your economy, gain early access to Iron, and unlock the Guerrilla II promotion. Then you might use FoL to upgrade your Lumbermilled Forests to Lumbermilled Ancient Forests, build some Disciples and upgrade them to Rangers (for the promotions they carry over), and unlock Woodsman II. Then you might switch to OO to eliminate unhappyness in one of your cities with the Tower of Complacency (the one where you're planning to build City of a Thousand Slums, of course) and to build an army of undead that can walk on water. Then finally you might switch to Order for its protection from a rising AC. This and other multi-religion gameplans require a fair bit of religion changes, which can add up to so many lost turns that they aren't practical - unless you have Spiritual. The savings also applies to Civic changes, which can also add up if you make them piecemeal, especially in the longer gameplay modes.
I don't see Tolerant as a "you must go conquer" trait, I see it as a flavorful element that arises when you are forced to conquer. The fact that there are some bugs that still need to be worked out (such as the 2 palaces exploit) should not be a reason to remove the trait - it should be a reason to fix the bugs. If you take a civ that does just fine without one of its traits, and replace that trait with a powerful one, then you'll be giving that civ a big power boost. I don't think the Elohim need or warrant that kind of boost, and so should not be changed.