When writing a novel, there a comes a point in the middle when you must evaluate what you intended a story to be and what it has become. A story takes on its own life once words are put to the page, sometimes that life is different then the one you set out to give it, much like the way children never follow the plan parents establish for them.
You can force upon the story themes that you wanted to include, but that's not my style. If the confines of the story don't make room for them, then my feeling is that they weren't meant to be discussed in that situation. As I continue to work on my new manuscript, I realize that one of the ideas that I thought would be central to the book is completely absent. Maybe in the past that would have driven me crazy. Stepping back, I now see those ideas were never really compatible and the ones that have replaced it feel more natural, and more focused.
Sometimes ideas are best left as ideas. Plans never work perfectly went put into practice. Writing is a survival sport...adapt or perish.