The Time of Troubles
The Time of Troubles was an exception to many of the normal rules for how deities work in the Realms. During the Time of Troubles, the powers of the Realms were forced to either place all of their divine power in one mortal avatar or, if they exist on multiple planes, were forced to create avatars upon whose existence their entire future divine connections to the Realms were staked. Since the powers of the Realms were forced to stake so much on their avatars, these avatars were acutely vulnerable. While the death of an avatar did not mean the death of the power (Bane and Bhaal, at least, went through multiple avatars in succession before finally dying), powers could only maintain themselves in one avatar form and could not connect with their homes and power bases in the Outer Planes (if they had them).
However, during the Time of Troubles, the general rule that only a deity can kill anything other than a demipower was not violated. Bhaal was killed by Cyric using the sword Godsbane at Boareskyr Bridge. Godsbane was Mask in sword form (evidently an avatar form of Mask). Thus, a power killed a power.
Midnight used a disintegrate spell to kill Myrkul in Waterdeep and then used a dimension door to move the dead avatar’s body over the Sea of Swords. At the time Midnight held within her some of Mystra’s divine essence, transferred to her through a pendant in the form of Mystra’s symbol that merged with Midnight’s flesh during her travels. So, once again, although through a slightly circuitous path, a power killed a power.
Mystra died at Helm’s hand on the Celestial Staircase, trying to gain access to her home plane. Before she battled Helm, she had transferred a great deal of her power into her Chosen, Azuth, the Magister, and Elminster. As she died, she gave Midnight the pendant with some of her essence and spread the remainder of her power into the magical weave that surrounds and permeates Realmspace. Elminster was able to call back a ghost of her presence as a sort of magic elemental to kill one avatar of Bane’s, but it was not strong enough to permanently destroy him, and his essence was able to be gathered together by Myrkul and then transferred to a new avatar. Ultimately, Torm killed Bane in Tantras. Again, in the cases of Mystra and Bane, one power killed another.
Gods who were dead at the end of the Godswar were dead in the Realms unless at the end of the Time of Troubles Ao reinstated them himself, as he did for Torm. However, only deities whose only worship ties throughout the many crystal spheres were to Realmspace could have completely died. Any deity who had ties to other crystal spheres would not have ceased to exist. Ao has influence over the powers of the Realms, not the panspheric and multidimensional universe. Rather, all divine ties between that power and the Realms would have been severed. The power itself would not have been dead, but might as well have been for any inhabitant of Realmspace.