I think whether the banning of genetically modified goods violates the spirit of free trade truly depends on the motives behind the ban.
We would never, for example, say that banning the importation of marijuana from some country where it was legal violated the spirit of free trade. So if the people of a country truly feel that genetically modified foods are dangerous, they should be able to ban their import. (They probably should ban them domestically as well, I'd say.)
However, countries often use issues like this as a "fig leaf" for protectionism. This can be seen when countries ban our beef, for example, because of alleged fears of BSE. You also hear accusations that our talk of limiting imports from countries with poor working conditions, for example, is a fig leaf like that.
So I think it really depends on why the ban is being imposed.