I think that by keeping the secret about their whereabouts, Luke and Ellie were more likely to stay together as a couple. They were joined by their lie and by the tragedy of Ellie's death. This probably kept them together as a couple longer than if their relationship had run its normal course.
Their secret also served to perpetuate distrust amonst the community. Luke and Gretchen knew that Ellie was at the river alone. They did not know that Falk was not with her. I think they may have always wondered a little bit if he had been involved. It looks like Gretchen was convinced it was suicide. Unfortunately, the rest of the town need to blame someone and they pinned the blame on Falk.
Luke's father always knew that Luke had some kind of secret and he always wondered if Luke was involved. The secret caused his father to have doubts.