Nauxus has to juggle his feelings for you and his duties as chief, it's another aspect present a bit of everywhere during the war, the fact he is always more eager and genuinely interested in spending time with you rather than dealing with the war. And again, he tries to keep you safe during the rogues'trial, he even gropes and admits he wants to "bed" and is interested in you romantically before going.
Thane's fate is not tied to either one, he either walks recklessly into the lizard tribe to be shot down or presumably gets left scarred emotionally by the chameleon and your choices (or worse), the game still lets you choose about pursuing Axel or Nauxus romantically even if you go down the appropriate routes, in case their methods were too unforgivable for the player.
And yes, the spy commits suicide, presumably to not be caught, probably part of his training, it is not stated explicitly.
What happens in the prisons is left to imagination, i personally just assumed the bulls were complaining madly due to their temper, the only thing we see is Axel deciding to kill three lizards just because (so Thane likely can't do anything about the prisoners).
Both sides were deceived by the chameleon mimicking the species and letting himself be seen to have each tribe blame the other for the kidnappings, it slowly escalated until it put the tavern at risk as well, and both chiefs had to come up with a final plan involving you... no side was willing to listen to nor send an ambassador, he'd have been shot down on sight or caught.
Another emblem was seen previously, buying everything is also fairly simple (2 jobs, love hotel, sleep, rinse and repeat for 7 days), and you can keep many saves just in case.
Regardless, no side is pure during the war, and each choice they make can be interpreted and valued in different ways by different people, i feel opinions change a bit after it ends, when you have the full picture and know why they behaved a certain way or if they manipulated at all.