What of my suggestion, where disaster-prone areas may provide minor passive benefits? (as I said, volcanoes could provide faith or something). Similarly, floodplains are very prone to flooding (in fact, people expected them to) but sometimes, they'd flood much more than expected and cause widespread damage. Rather than positive 'disasters', what if the trade-off was slight bonuses throughout the normal game?
Sorry, I thought I was including such mechanisms - for instance, in that Volcanic soil around a volcano is very rich, so settling next to a volcano gets you extra For production on X tiles, but an occasional Eruption that Pillages one of those tiles. Floodplains are notoriously rich soil (already reflected by the factors in the game on that terrain-type), but occasionally the flood gets out of hand. That could give you a Eureka for Irrigation, and in the Industrial Era, the ability to 'canalize' the rivers, building levees and otherwise improving the banks s that they don't flood as often. This was done to almost every river in Europe and North America, and it also had the benefit of improving navigation on the rivers, so (in game terms) giving, perhaps, a bonus to Trade Routes/roads along rivers, or Gold from the traffic.
Even catastrophic single Events, like the Bubonic (Black) Plague that drastically reduced the population in Europe in the 14th century CE had a 'positive' side: labor became so scarce that even the lowest members of society, peasants and serfs, were able to demand higher wages and improve their living conditions. It has been argued that this realization by 'the lower classes' that they had some economic power led them to start demanding political power as well - like Guilds and Associations. Potentially, then, Plague 'disaster' Events could give Bonuses for certain Civics, or even Technologies - Machinery to replace the recently-deceased labor, for instance.
Maybe some of the "benefit" of the natural disaster is how negative it is? The Abrahamic flood myth can be traced to an early Mesopotamian version. Mesopotamia was incredibly prone to flooding around the Euphrates, and the culture and belief of the people formed around this, converting the "natural" disaster into a "divine" disaster. Maybe serious disasters result in an equally serious reaction from your people in the form of a boon for you.
Example: In response to a flood, you get a chance at discovering a great work of writing in the form of a flood myth (or maybe it counts as a relic). Maybe your people interpret a volcano, flood, or fire as divine retribution, and in response become more pious (bonus faith generation or extra religious pressure for X turns). Maybe the response you make to the disaster gives you an opportunity to earn an effect (the Vox Populi mod implemented this) and if you respond well and save your people from destruction, you get increased loyalty or free era score. All sorts of interesting things can happen in the wake of a disaster.
In fact, quite a number of Great Works can be considered as 'inspired' by Disasters: the writings of Boccacio by the Plague Years and the paintings of Bosch by the famines and pestilence of the Middle Ages. So, in addition to potential Religious Bonuses from Volcanic activity, Floods, Earthquakes, etc. there might even be a potential for a 'free' Great Work inspired by what your Civilization just went through. This could even be extended to In Game Events producing Great Works: bomb a city and possibly produce Picasso's "Guernica" or "The Leningrad Symphony", for instance...
As far as balance goes though, I don't think we need to have expressly "positive" natural disasters. A disaster to your enemy is a boon for you! The Japanese talk about the kamikaze (divine wind) which wiped out a Mongol fleet that was trying to invade by sinking all of their ships. Sure, the Japanese islands are prone to monsoons, tsunamis, volcanoes and earthquakes, but your enemies could be equally screwed by disasters as well.
I'm sorry, this won't fly. To the gamer, the 'disaster' that hits his AI or Human enemy doesn't matter: what he notices and remembers are all the 'random' disasters that hit Him!
As an example, years and years ago there was a 4X game based on Star Trek called "Birth of the Federation". It had a lot of faults, but the worst was that
all of the Random Events were Completely Disastrous: A Borg Ship wipes out your Fleet, a star system you are exploring is home to an Isolationist Master Race that destroys your ship and your nearest base, etc., etc. The fact that all this might happen to another faction in the game didn't matter at all: after a couple of attempts at playing, Everybody turned off Random Events - and left them off.
Having wasted time and money on that game, I say again that the answer is to have both negative and positive aspects to any 'Natural Disasters' included in the game, and I think we are on the way to coming up with an interesting set of 'positives' to the 'negatives': better tiles near a danger spot that partly compensate for occasional destruction/damage caused b Earthquake, Flood, Volcano, etc. a positive reaction from your Cv in the face of Disaster in the form of Eurekas or Bonuses to Loyalty, Production, Civics and Technologies, even "Disaster Inspired" Great Works...
In every case, there has to be some element of Decision by the Gamer - do I risk settling on/near the Floodplain, Volcano, Disease-Infested Swamp? Do I respond to Disaster by ignoring it or making a major effort at recovery that may give me extra Benefits from the population to offset all the resources I throw into the recovery effort? - It is always a better game if you Feel you have some control over what happens as opposed to merely suffering through what happens with no possibility of affecting the severity or frequency of the event.
