Alon Ghemor was apparently assassinated in 2379, according to "The Calling". Of course, "The Calling" doesn't sit
entirely comfortably with the "mainstream" continuity, though I find a ways to handwave and add it all up.

If not, the Vinculum is a perfect excuse to have it take place in another timeline. It is known that Ghemor was definitely assassinated in the mainstream timeline after 2377 but prior to 2381 (the mention of his assassination in "Destiny" I assume is indeed a reference to "The Calling") because as you say a new Castellan is in power. She hasn't been named yet- though the Star Trek Online book does name Natima Lang as Castellan at some point. Who it is in the mainstream continuity remains a mystery. I tend to doubt it's Lang, personally, as she would surely be far more open and progressive than this castellan, who seems conservative and somewhat isolationist? My totally personal guess, if it is someone we've seen before, would be Malyn Ocett. We still don't know yet, though.
PS: Why was Ocett my guess? Well, we know she's a bit of a xenophobe, so the more isolationist, less Federation-friendly stance in 2381 fits her style. She was a member of the Directorate, yet "A Stitch in Time" also established she was shaken and strongly affected by Parmak and Ghemor's rhetoric. To me, it seems she'd be a natural to assume command of the government in the aftermath of the supposed civil war post-Ghemor. She could reconcile the Directorate and Reunion parties, and her military background would appease the Directorate extremists, while Reunion leaders like Garak retain high-profile positions.