I have a situation in which I need to save up iron bars for a technology, but my most expensive crafter recipe uses more iron bars than I can produce and I cannot turn off the crafter. I could get around this with a market, theoretically, but did not get any at this point. I deactivated the auto-smelter advancement so I can save up iron bars, but it would make sense to me that if you manually deactivate a crafter or smelter it won't automatically reactive itself.

The only thing you can do right now is choose a recipe that will keep the crafter busy for a while so that Auto-Smelt can't activate (because no crafter becomes idle). Manually deactivating a crafter is exactly what triggers Auto-Smelt, so I don't see an option to change Auto-Smelt in this regard. Furthermore, all Auto-advancements are a bit stupid, so, that's nothing new.

If I understand it correctly it hás to work this way because of battles.or else when you get nuked, it wouldnt reactivate.

Exception: Auto-Draft, that's the only Auto that won't cripple you if you're not careful.

Auto-Conquer is useful for clearing out territories when you have lots of experience on a map, are confident you've got enough armies/money to clear the level and can throw caution to the wind and let the dominoes fall, notably late on large maps like Trisk, USA, EH.

For all others, leave them disabled and only enable in specific scenarios for specific durations of time.

They're useful for WZIB & WZIC, and really that's it.