There was a time when Jane Shepard had held his everything, making him fearful of death, when he should've been welcoming it. Thane should've been praying to all the gods for the salvation of his physical body, but instead, he loved Shepard. He loved Shepard like the rolling sea was blue, like the stars were never to be counted. Loving Shepard was like breaking through doors with your head and watching your race fall, while being held with the clouds on high, surviving for that one person.
Shepard's heart was not his. Not anymore.
As he watched, observing the blossom of undeniable love between two spectres, Shepard and Alenko, Thane was confined to silence. In an attempt to rekindle their once burning passion, Thane became the protector of Kaidan, for Shepard's sake. And while this was the opposite of his desire, he was unable to decline the offer, of which he himself had given her.
Later, when time had slowed and glass gathered in an intricate dance of sorrow, Shepard rejoiced in Kaidan's healing. They had proved themselves, in Thane's eyes, to be a true symbol of undying love.
So the prayer said on Thane's death bed offered Shepard not only to the gods, but to Kaidan as well. And to Kaidan she would run; as a lover, a sister, and a companion.