That is correct. The EU has two issues at hand here - first, protection of its market, i.e. the (principally) French farming cartels' market from U.S. competition. These are heavily unionized and very politically influential and they export to Africa in direct competition with cheaper (and more robust) U.S. GM drops. And second, protection from competition from African farmers. The issue there is that they fear the latter will use GM grain as seed crops (it isn't uniformly sterile), grow it on their own, and end up competing with the EU crops.
The "threat" to which you allude is a real one - a total embargo on the importation of African crops because of suspected "contamination" by GM grain. The African farmers have a hard enough time as it is competing with subsidized competition (both the U.S. and the EU subsidize farm products) without being threatened with this.
What is pernicious about all this is that the one hope African people have of becoming self-supporting is free-market farming, the very thing this EU policy is killing. This is not a benign policy. It keeps the Africans dependent and it forces them to choose between starving today or starving tomorrow. It ends up, ironically, forcing their governments to accept grain from the U.S. for free, which is well-intentioned and necessary to solve the short-term starvation problem, but only makes the long-term problem of self-support worse.
It should be remembered that the very same people in the EU who criticize the U.S. for being selfish and unilateral are the ones doing this to the Africans for reasons that are nothing more than selfish and by policies that are nothing less than unilateral.
Environmentalism/Sustainable Development is the Highest Cause, it trumps all others.