As the film plays, the audience never got to see all the cut scenes between Barnabas and David - most of their relationship is simply implied by what others say in their scenes when referring to it (which is a real shame - but we've gone into that recently, so I won't rehash). And the only thing that the audience is aware that Barnabas witnessed with regard to Roger and David was Roger having David guard the room while Roger made out with the coat check girl - Barnabas didn't even see Roger going through the guests' coats. Yet in the scene in which Barnabas gives Roger the choice, Barnabas specifically speaks of Roger's "thieving, selfish life." That certainly indicates that somehow Barnabas is aware of much more than the audience is aware he is, and it would seem to imply that there may have been a cut scene in which at least some of the guests discovered that things had been stolen from them and somehow Barnabas was aware of it and perhaps even took care of it with a bit of his hypnotic powers. And there's also how Barnabas says he's going to give Roger a choice despite the fact that he finds doing so "so repellent that it sickens" him to his "very core." That brings to mind that quite possibly the spoiler that said that in the film Barnabas plans to kill Roger but someone talks him out of it may have indeed been real. Perhaps Barnabas expressed his outrage over Roger to Elizabeth, and while doing so he threatened to kill Roger, but Elizabeth talked him out of it, and instead it was decided to give Roger the choice.
Unfortunately, though, there's nothing more substantial than a few inklings in the film that any of that might be possible, though I do suppose the inklings are there. But sadly, as things stand in the film, it's completely up to the audience to piece the depths of the Barnabas/David and Barnabas/Roger relationships together by simply using dialogue and situations that mostly hint at them rather than expressly describe them.