We're seeing intelligent purposeful behavior from the "essence" of a man who has left his brain far behind. Beaming him back from pure energy goes with the territory. Sometimes in Trek you just have to suspend reason.
Here's the problem with the suspension of reason for this particular episode. If the drama of the main story line is centered around elements that are understandable (i.e. Picard acting strangely, crew having doubts, a mysterious entity that can hide in anyone), and than have the climax resort to something that we cannot understand (Picard magically entering the Enterprise's systems), you are short changing the audience. Suspension of disbelief normally works when the whole story requires it, not when the story needs it to resolve an issue that didn't require it.