Imoen didn't auto-disintegrate when she died because in BG1 she wasn't a Child of Bhaal, and when they decided to retcon her into one in BG2, they had no means of addressing the fact that it was already established that she could be they just shrugged and ignored it, which was probably the best option they had.

She was never a contender for the Goddess of Death because she didn't want to be. If she's involved in the plot of ToB at all, it's about supporting CHARNAME's candidacy. Nothing mechanical was stopping her from being the one to ascend.