GMOs should certainly be regulated for safety and transparency, which is part of the job of the FDA in the United States.
Dekhn's statement in the comment about the allergenicity was this:
A gene from Brazil Nuts that coded for a protein high in methionine was cloned into soy plants; soy from the resulting plant caused allergic reactions in subjects.
An important missing part of that ...in subjects with an allergy to brazil nuts. In otherwords they found some allergic reaction to the brazil nut protein in people allergic to brazil nuts. It did not create an unknown or novel allergen (although allergenicity should be a standard test for GMO food products).
For 8/9 subjects it was not the primary allergen (and for one it was the allergen that causes a dangerous reaction). Regardless an allergen is present and it is good that it was identified. The paper concludes with this:
"It is prudent to assess the allergenicity of proteins in transgenic foods if those proteins have been derived from sources that are commonly allergenic. The use of currently available animal models alone to predict allergenicity in humans does not produce accurate results. Techniques such as radioallergosorbent tests, SDS-PAGE with immunoblotting, and skin-prick testing can identify IgE-binding proteins that are probable allergens in transgenic foods derived from sources known to be allergenic. This strategy will not be useful in assessing the allergenicity of transgenic foods in which the allergenicity of the source of donor genetic material is unknown. Most current applications in the field of plant biotechnology fall into the latter category."
There is no doubt (in my mind) that GMO needs to be regulated and reported. If there is any protein from an allergic source that source needs to be listed on the food product specifically as "contains material from X" -- in this case X = brazil nuts.
The fact that the source donor material could be unknown (proprietary secret) is completely unacceptable. The FDA should have full regulatory control over GMO and they should be treated with a scrutiny closer to drugs rather than food. There should be absolutely no "proprietary secrets" regarding the source material or process used to make the modifications. There should be complete transparency and rigorous testing for allergic potential.
Maybe increased regulatory control is all that GMO doomsayers are after, but I think the hyperbole hurts their argument when there are sound scientific arguments for increased transparency and regulation.
tl;dr: This is a legitimate concern that should be included in a regulatory framework that supports safety and transparency.
There is still a small chance that someone who did not know they were allergic to Brazil Nuts but already consumes soy products could be impacted by the new product. However I am not sure how to mitigate that and still have GMO food products. From a consumer perspective they could be introduced to allergens that are now present in their "new" existing diet. I would sympathize with a consumer who said "hey I did not change anything and now I am impacted." So in this case labelling would be insufficient. Perhaps the answer is to say that "known allergenic introductions" are not allowed for GMO food.
Many benefits and concerns lie ahead. In such cases, for their sake, the consumer needs access to valuable information.