[LDiCesare]

Burden of Time shouldn't be an issue. You can Dispel it. You can also probably get everyone but Atlantis, Ermor and such long lived races to contribute so you can cast it with an additional 999 gems and be sure it's dispelled. You can also try to kill the mage who cast it, for instance by spamming earth attacks and other assassination spells on the province the caster is in.
You can also use boots of youth, rituals to resuscitate your D mages to simply counter some of the effect.

As for the general suggestions, there's a game called threeforts running with settings that look like this. But even then, the most gamebreaking spells are master enslave and all the teleport-like spells.

Offensive globals: Not really a problem. People who cast it will get ganged upon, enchantments will be dispelled. Even a lot of Armageddon wishes doesn't ruin the game. These are good imo, as they can help end the game faster.

Gem rituals: Well, they give a boost to the nation that can cast it indeed but it's an investment, and can be dispelled. The players who can put them up and keep them deserve the gems. They are somewhat unabalanced because if you get a capital revenue like MA Mictlan you're less likely to cast such a spell than if your revenue is all nature for instance, but nations can be balanced in other ways.

Remote unrest spells are about the only way to shut some capitals, and you can put up domes to prevent these. That's really easy to counter in important provinces (domes) so it's not an issue.

Assassin spells are a pain but bodyguards, bottles of living water, domes, all help. Assassin spells targetted at a SC that just conquered a province are much more painful. This is the only suggestion that I might agree with. Even then, there are counters (teleport/cloud trapeze a SC and then give orders to attack to 10 scouts into that province so the scouts get targeted, not the SC).

Overall, there are counters to all spells. There is strategy in countering them. There is strategy in researching them, making sure you don't spend your gems on something else, making sure you have a caster that can cast them (Flames from the Sky's not everyone's spell for instance), making sure you spend enough gems to not get dispelled, or that the dispellers will waste more than what you invested...