Agais felt he had to apologize for the actions of the Horde, not that Jaina would know what the Horde, Garrosh, Outland, Blood Elves or even Theramore are at this point.

Well, Stormwind had already fallen to the old Horde and then the orcs were all put into internment camps well before that point, so she’d know of a Horde…just the ‘wrong’ one.

…And now I’m wondering just where Thrall’s escape falls on the timeline.  Before the Scourge plague, and thus the Culling?  It doesn’t make sense for it to be after…

Yes. Assuming the CoT instance is canon, Thrall’s escape happens before the Scourge plague since Kel’thuzad is still a member of the Kirin Tor. It happens sometime after Jaina and Arthas become a Thing though.