I understand from a role-playing perspective. It makes sense from a technical perspective, but not from a role-playing one.
By the time Kivan would even consider sleeping with the PC, he already knows that Deheriana is not in Arvandor/Arvanaith waiting for him. What are Kivan's expectations of the PC's fate? Does he expect that the PC and Xan will eventually be united in Arvandor? If so, then there is no way he should ever even remotely consider a PC romance in ToB.
From what I understand, does Xan even believe that he and the PC will be united in Arvandor? He seems to feel that this right will be denied her based on her parentage. If he does feel that they will eventually be united in paradise, then yeah, it would be as wrong as wrong can be for any sparks between Kivan and the PC. If, however, Xan believes that he has bonded with a woman who will be lost to him forever following her inevitable and looming demise, and if he manages to convince the PC of this, then she'd have no reason not to take comfort with Kivan. After all, if Xan has managed to convince her that she's never going to be joined with him in Arvandor because her father is Bhaal, why shouldn't she enjoy what little time remains to her, by Xan's own predictions.
This gets complicated. Especially when you take the sense of betrayal she must feel into consideration. When someone that close dies, there is a sense of betrayal, that they abandoned you. IRL, it can drive the recently widowed into new relationships (usually unhealthy ones), far before they are ready for it.
I'm not making a case for excluding bonded Xan/Kivan. If you say it wouldn't work, who would know better than you? I'm just saying that this is a really complicated issue!