For the first: Emet-Selch is tempered, as is Elidibus. Mitron might be tempered as well, and the same might hold true for Fandaniel. This has not stopped the Scions, the WoL, or Ryne from attempting to reason with any of them. Likewise, Tiamat was explicitly tempered, aware of this fact, and unwilling to free herself from her bonds out of the belief that she would fall sway to Bahamut's will if she approached him. This carries the strong implication that she is not currently under his control, and is able to think and act for herself. And even before all this... recall that Lyse was willing to entertain the notion that the Qalyana, despite being tempered to Lakshmi, were still worthy of consideration and so invited them to join the summit held in Ala Mhigo to help decide how the nation would be governed going forward. And even though that backfired on everyone involved, nobody ever said Lyse made the wrong call in giving them the opportunity to be heard. Nor did she stop trying to make peace with the Qalyana after the fact, even though their current leader from that point on—the resurrected daughter of the previous leader—literally has no soul.
If the protagonists are willing to give such consideration to the tempered, despite the previously held belief that they had to be killed on sight to prevent further primal summonings, there is no particular reason why someone like Emet-Selch would refuse to do so despite having a much clearer picture of what being tempered actually means.
As for the second: I would recommend rewatching the cutscene after the Shiva fight. In it, Ysayle echoes Hydaelyn's own catch phrase and a particular verse from Answers, strongly implying that, like the WoL, she'd been in direct contact with Hydaelyn on at least one occasion. Her end goal, which remained the same from her first appearance all the way up to her death, is similarly in line with what Hydaelyn would surely want: An end to the Dragonsong War. Another thing to keep in mind is that Midgardsormr is explicitly bound to act as Hydaelyn's servant, yet he made no effort to stop Niddhog's Horde from descending upon Ishgard, nor did he ever come to the city's defense over the course of 1,000 years of bloodshed.
There is a strong enough implication through Ysayle and Midgardsormr's actions to suggest Hydaelyn had written Ishgard off as an acceptable loss if it meant putting an end to the conflict it had brought upon itself. And it's not hard to imagine Hydaelyn would view things that way, knowing what she did to the old world in pursuit of containing Zodiark. And while we came to Ishgard's defense, we had to do so without Hydaelyn's Blessing.