There are a number of factors that must go into the decision of a countries banned imports, the majority of these decisions being based primarily on economic standing. Technology (such as GMO's) promotes increased productivity, and this kind of innovation is the goal upon which free markets are built. That being said, not all Nation States are free markets, and the majority of these States functions function independently of the others. Thus, innovation developed in one country could have severe economic impacts on the effect of trade in another.
Farmers using GMO seeds can produce much higher yields at much lower costs, now if these crops were to be imported into a country producing the same crops with non GMO seeds at a absolute and relative higher cost (more land, resources, etc..), the farmer importing would be at the clear advantage and would eliminate competition. Thus what has effectively happened is that the free market of one state has impeded on that of another, and this gives all the benefit to one state with none to the other, and should be allowed to be banned by the latter's governing body.
On the other hand, there is the argument that in the cases of relief and 3rd world countries that are underproducing, these bans should not be allowed. This is where the line is blurred because in some cases and to some extent they should still be allowed (going back to the idea of long term imports impeding on the nations own economy and production levels), but unfortunately there is also a high level of corruption in many of these states leading to many decisions being made in benefit for the few and wealthy rather than for majority living under poverty lines.
The last argument to be made is the argument for GMO's leading to not higher yield crops, but improved crops with higher amounts of micronutrients, i.e. "golden rice" with increased levels of beta-carotene. Again here the lines are blurred, and one must consider who is really deriving the benefit from the crops. In some cases of extreme malnourishment, an increase of beta carotene in diets already lacking the majority of other nutrients will still only harm the economy more than its benefits of improved vitamin levels will help.
Thus, many different sides of many different arguments must be taken into account for each individual state / union. But overall, I do believe that the ones making these decisions should be the individual states themselves, and they are in fact justified in banning imports of GMO's.