On Heroes: At game start you have two kinds of Heroes, your basic regular heroes that begin at level 1 and then "Champions". Champions are always shown on the map because they are famous - they are very powerful and they work for a nation. Which means instead of following one of the three hero AIs they follow the commands of the nation's leader. Heroes can become Champions later in the game, and you can also "disgrace" Champions back down to heroes.
In the North Burns the game currently starts with 30 heroes being randomly spawned, this number is absolutely subject to change and is still being balance. Right now I'd say about 2-3 of them die to random causes, and another couple end up too critically injured or mentally unbalanced to be effective, so its a little over 10% that will get neutralized without your interference. If I play to just throw up random obstanes everywhere I get that number up to 30-40%, but the Heroes that survive are stronger for the challenges and level up a bit faster. We wanted it to be tactical in who you pursue, and what objectives you choose to defend.
Avoiding a group vs dealing with them is actually an answer I can't give, I'm not sure what the ideal strategy is. If you just pursue your own agendas you'll bump into enough heroes that you don't have to go looking for them, which often leads to that scenario where you are plagued by 3-4 recurring Adventuring Groups which you end up handling, but then there are some other heroes who have little idea of who you are but get summoned in to help when an Agent's threat gets too high.
I will say that having a balanced view of the world through infiltration is essential to finding and targetting the groups that are working on campaigns you want to stop. To give an example, there is a long campaign that returns the dwarves to their homeland in the mountains north of Cylaria - if this happens they begin to upgrade the weapons and armor of Cylaria, they fix the High Gate and close it to your minions, and all adventurers involved get a perk. Very, very, very bad - especially if you are going a war route through the north. The process of this campaign involves a hero meeting with the dwarves down south, then a grand meeting of adventurers, then they go off to get some artifacts, then they go to the mountains. Havin infiltration at ANY of these key points, or on ANY of the heroes involved, or on the KIGNDOMS that the heroes ask for help from will let you see this campaign is going on.
Heroes in the right configuration and level are difficult to kill by standard agents - but if you come at them with The Baron and some Giant Minions you can pretty much crush any low-medium hero with ease, and then a higher level hero might flee with an injury (which is semi-permanent). Heroes (and Agents) heal slowly over time, so wounding them is a great way to get yourself some breathing room. If you played the game to Kill Heroes, you'll be able to "build" an agent appropriately - there are also agents specifically meant to murder heroes and they are very good at what they do.
You can't ever "be a good guy", this was part of a system that we lost because it was too complex (though it will be a stretch goal for KS). However yes you CAN trick the heroes and other nations into going after other benevolent powers, especially if the cultures hate eachother. However, Agents can be seen as allies of a nation and heroes - they can gain "Welcome at Court" which means they are friends of the nation, and they can donate gold, food, and even mercenaries to show their support for the king and gain some influence. One of the main benefits of this approach is that if a hero comes tot hat kingdom to say "that agent is working for a dark power" he may find himself ignored, jailed, or even beheaded. In addition, if you get attacked there, the Royal Guard will come help you in battle.
Jalak you really nailed our idea behind the Alliance - it is a response to something dire in the world, but to those who don't share the same belief they look at it with suspicion. This is the suspicion you need to leverage to ensure that the Alliance remains as weak as possible, and you also don't want to be too overt with your powers which may convince the other nations that they are also under great threat.
The Alliance can target a mundane threat, and then dissolve - it can also simply dissolve under discord and lack of threat which makes nations hesitant to form an Alliance in the future.