I didn't find it that big of a leap. The date on the picture, Tori's panic to flee Salem, proximity to DiMeras, Paul's father dying "before he was born," coupled with John's embrace of Tori, led Will down the path.
Marlena knew everything Will knew except the embrace, then found out John was involved with Tori during the timeframe (and again I state they could be more up-front with this, as it could work with the established timeline). She knows when she and John were together and would have known the date on the pic corresponded to one of their "off" periods (per my speculation around the time between Izzy B and Rebecca, although at that time there were no DiMeras in Salem yet, and Kristen was just about to come to town).
It would have been nice if the writers had had Will ask, "Grandma, you were in Salem at that time, do you remember her? No--what about John? Oh, you and John weren't together yet? Etc." But that would have required actual planning and forethought.