Any decision you make has consequences, not all of them good. Ian and Barbara are a special case because they did not choose to travel with the Doctor, but other companions did, sometimes more then once (choosing to travel with him even when they could safely get home like Jo and Sarah). Vicki wanted to remain behind in Troy which was just decimated by war. Life at the time was much harder then what we're used to. If her future life was unhappy, is it the Doctor's fault?

I wouldn't worry too much about Ian and Barbara. They have each other. That helped them through a lot worse then a few awkward explanations.