Yeah, Thordan might not have been out right evil but he was seriously misguided. Its worth noting that we don't specifically kill him either. When they lose the primal form he and all the knights dissipate into Aether suggesting its more likely the result of the summoning failing. Side effect of turning into a primal maybe?

Regardless the very fact he was in Ahys Lla indicates he was after more power. He was already a primal and already had the Eye. Ahys Lla offered him imprisoned Eikons to syphon off. I cant see why else he would have been there. That's crazy dangerous.

We are also very different from the Ascians. The Ascians goal is to return Zodiark and everything can be sacrificed to reach that goal. Further they seem to generally have contempt for the mortals of Eorzea. The WoL on the other hand constantly struggles and sacrifices to help the people of Eorzea, even when it forces is into crazy dangerous situation and situation which some would consider demeaning considering our strength. We had no obligation to Ishgard and further many of them have been unhelpful and outright insulting to the WoL. Never the less the WoL has gone out of their way to protect Ishgard and its people even when the blessing of Light was stripped from them.

As for the Beasttribes, the very fact we oppose the Garleans is in a large part due to their desire to genocide the Beasttribes. Further we have generally been pretty selective in out attacks on Beasttribe holdings. The most serious campaigns the WoL wages against the Beasttribes are for factions within the beast tribes and they are generally to oppose oppressive, cruel and corrupt factions and/or to try and break the cycle of violence between the Beasttribes and the city states. (On that note, its one of the reasons I liked the Sahagin story the best. Novv is a legend.) When members of the Beasttribes are being abused by people from the city states we even intervene to protect them.

Finally, I don't think Ishgard is now a democracy. Its still ruled by the High Houses and Aymeric is simply standing in for the Archbishop, a role it seems his father hoped he would take up eventually. I actually suspect we will eventually see Aymeric become king. There are too many 'throne lies empty' and 'Until a true king arises' comments in songs and cutscenes of the past to make me think that's not a thing. We haven't even truly dealt with the social equality beyond baby steps.

Further while Nidhogg has returned, the Azure Dragoon isn't dead and I suspect we will be able to pull him out of the new Nidhogg (ie. enter the soul of Estinien using the echo and drive Nidhogg out. Bonus points to SE if the combat scene is a memory of Estinien's destroyed home.) Further the Alliance is beneficial to Ishgard as it give Ishgard support from the other member states. If Ishgard is threatened the other city states are now obliged to take action and lend resources. Ishgard wasn't immune to the Eorzean political scene. 2.55 showed that. They weren't force into it either. Their reason for avoiding it before was one of pride and arrogance. Most ironically the Ishgardians established the first Eorzean Alliance.

Even the issue of growing too powerful has been raised before in the story. The original EX primals showed that effectively the Ascians forced us into an arms race with the Beasttribes because we couldn't just leave primals alone. Doing so would be devastating to both the beasttribes and the land itself.