I think it's important to remember that a portrait records, primarily, the subject's response to the photographer. Therefore, the photographer (and his/her expressions, words, body language, tone of voice, pace, appearance, etc) is as much a part of the photograph as the subject.
There are plenty of examples of portraits which are brutality honest and not beautiful, and because of that are very successful. You always must keep in mind your end goal. If you are shooting commissioned portraits for a family, then yes, you will probably need to be sure the images are flattering and present the subjects in their best light. However, if you are shooting portraits to sell in a gallery (for example) you have more flexibility to shoot in whatever way you feel shows the character or the moment most effectively. That was the case in my "regulars" series; they aren't designed to be flattering, but rather are basically raw character sketches.
When you realize and accept that the photographer is ALWAYS part of the portrait, it becomes easier to flex, tug, and coax the life into the image.