Jonathan Is already trying to facilitate a serious romantic relationship between her and Desmond with the intention of getting Desmond to have a child to continue the genetic line of Paragan.
In due time he manages to arrange and facilitate their secret relationship, pretending to be in relationship with Gloria himself in order to cover for them. Thus, it is easy for them to claim later that Jason--who looks like his mother and not at all like his father, except for his eyes which Sen'tran alters to look like Gloria's eyes-- is truly the son of Jonathan.
Although Jonathan Married Sharra and had children with her, he did so only for the sake of having children. Jonathan is strongly same--gender attracted for genetic reasons, and has no great desire for a physical relationship with a woman. When he marries Gloria later it is for the sake of Jason, and their relationship is never sexual. They were always very good friends, but loved eachother almost more as siblings than as lovers.
Gloria, however, has no desire for a romantic relationship with anyone other than Desmond after Desmond is lost, and Jonathan, having been raised Paragangian, is determined not to indulge in his same gender attraction.
Hope , the child Gloria has after Desmond's return is the biological child of Jonathan, as Desmond made love to his wife using Jonathan's body before Jonathan disconected his spirit from his body, so, before the body became Desmond's body. This hope was the biological daughter of Jonathan, Not Desmond. This is very apparent in her appearance as she closely resembles her father.