We have had this happen many times (we have had 9 toddlers), so we've had lots of time to try many different methods to get it stopped. It was pretty important for me, because I come from a disciplinarian home and am pretty big on discipline. Like you, I didn't want the lap thing to become a habit. So I will report on our experiments.
None of them really worked. The most effective method seems to have been the waiting method. Each of the training methods that we tried basically failed until the child turned a certain age and then the methods seemed to finally work! (HA!) So the last few times we've tried skipping the methods and enjoying the lap baby (my husband really enjoys this closeness and feeding the baby). This seems to work just as well. So, while I don't really have a solution to your present problem, I can assure you that you are not creating a habit that will be hard to break. Our 10,9,6,5 and almost-3-year-old are all eating in their own seats at our family dinner table (as are their older brothers). They don't even want in anyone's lap.
I should add that they are only allowed those 2 options--their own seat or a lap. They are not allowed to walk around eating or take food into another room of the house. The car seat and the floor (sitting in one spot) count as their own seat.