As for ur answers OP:
*Amaljaa:
1.She's not executed due to the relationship of the U tribe and the Immortal Flames, its very possible that the U tribe members whom we freed for BoA daily recognized she's still alive although may beyond cure. To kill her will have a disastrous effect to politics. And i believe she might be an "experiment guinea pig" to cure primal tempering.
2.At the BoA quest from recognized to friendly, imma sure u forgot the tempered IF guy who can bluff and lie about his loyalty to ifrit but acts normally like a normal peep. Not to add that the beastman tribes (Amaljaa, Slyph, Ixal, Kobold) were "tempered" differently from the 5 playable races. Theres a HUGE difference and effect from being tempered as a faithful servant who might sacrifice themselves to give powers to the primal extreme awakening and a slave