That is a personal decision. We still allow dessert, however we KNOW that our kids aren't holding out for the dessert - but the theory on still allowing it, is that it isn't a reward for eating their dinner iykwim - because then they could think that healthy dinner is so yukky that you get a reward for eating it iykwim.
We have major eating issues in this house (and growth issues, all being investigated currently by the paed). We have been instructed to feed our 2.5 yr old when she is hungry - even if it means modifying the foods on offer so that we cover the food groups via the biggest meals of the day (difficult when there is no pattern to when she is hungry). So snack int he morning might be frozen peas, sandwhich meat and some fruit for example. Does it really matter what is eaten when, as long as the nutrition is covered? (Note here, my kids weren't filling up on milk or junk food as a replacement, they just weren't eating at all).
What it come down to is - how poor has the eating become, are they filling up on other things, is there any concern about growth/development, what do you want as the rules for your family (here, I fit into the not many rules category), and is it a battle you are willing to fight long term. If you try to force kids to eat more it can back fire and result in even lower food intake.
Just wanted to throw the other side of the story in, since we have spoken at length to both the paed, and the feeding clinic (dietician, occupational therapist, speech pathologist). 14 mo DS is now eating well (but won't eat veggies with dinner, but I sneak them in raw via snacks). DD is eating a bit better too, but still isn't growing, last weigh in at paed had actually lost weight.
This for DD started as refusal to eat much dinner, but became constant meal skipping, a good meal was 5 mouthfuls, often skipping more than 1 meal in a row (so could possibly not eat from 3pm til 11am, and then still only eat a few mouthfuls) and went on for months and months before we sought assistance from medical profession. DS refusal to eat was reflux related, but whilst his reflux is under control, he is actually doing quite well.