In regards to Lyse and the ananta, it was already established way back in the ARR storyline that tempered can infiltrate normal spoken society as long as they keep their zealousness under control long enough to accomplish their task (an ARR main scenario quest involved tracking down suspected tempered infiltrators at Little Ala Mhigo who had managed to fool the guards long enough to enter the compound, and eliminating them once their identities were confirmed - this probably also explains how they're able to keep abducting Ala Mhigan refugees in the FATE 'Taken', at a glance they look like any other person as generally a basic amount of tempering does not physically alter the body.).
Of course, there are exceptions though: the 'touched' sylphs for instanced physically turn purple simply by being tempered, and Sastasha HM showed what happens when someone is over tempered - they physically alter form into something vaguely akin to the Primal who did it (the Serpent Reavers and their captives turn into fish hybrids and the enslaved women become lamia - Captain Madison in his case becoming a Pirates of the Caribbean-Davy Jones-esque squidman).
Also, and this is another fact that is overlooked, is that tempering does not actually even require a Primal to be summoned again to temper new followers: when a Primal is summoned and then destroyed it leaves a lingering trace of it's aetheric energy in that area, which it's followers then gather up and immerse captives in (a twisted reflection of religious baptism?), having much the same effect of tempering as if the Primal themself did it. This is not as perfect as the Primal doing the tempering though: the sahagin beast quests in Western La Noscea showed tempered sahagin immersing captive Maelstrom soldiers in Leviathan's essence at the water's edge, and several you get to are 'drowned' and thus attack you, but several it has not 'stuck' and thus are saved.
This process also has the effect of physically altering the surrounding environment - this is why Zaha'rak is so barren due to the cursed torches lit by Ifrit's flames the amalj'aa have scattered everywhere it is now probably more barren and lifeless than the rest of Thanalan, similarly thanks to the drowned sahagin Halfstone in Western La Noscea now resembles the sea floor with even inland mountains encrusted in brine, coral and all manner of sea life due to Leviathan's essence, and, the Slyphlands in the East Shroud are slowly being corrupted by Ramuh's essence: the tempered sylphs using strange apparatuses to spew forth noxious fumes that contain Ramuh's aether which is poisoning the surrounding forest (and slowly tempering the 'normal' sylphs who are captured by their indigo brethren.
Thus, with all this established, Lyse is off the hook for responsibility as far as the events of the ill-fated conference in Ala Mhigo went: the ananta were simply not taken as one of Lakshmi's 'dreamer' until it was too late: anyone in her position would have acted the same.