The fact that he is holding a pillow is an ominous sign; a father in a similar situation, Earl Detraux, had smothered his severely handicapped son with a pillow. Shawn notes that his father sounds exhausted; perhaps he has come to the end of his endurance, and is prepared to end it all for his son. It is clear that Shawn's father loves him, and believes that his seizures are very painful for him. Perhaps when that final seizure strikes, he will kill his son to end what he sees as his terrible suffering.
On the other hand, Shawn's father's words show that he is still unsure as to what is the right thing to do, so maybe he does not kill his son at the end of the book. There is a moment where Shawn's and his father's eyes lock, and they