Well, here's the thing. In the original Silent Threat, the GTI was incredibly incompetent. They botched the coverup twice, and they deployed the Hades to act essentially as a sitting duck. This doesn't make for a terribly good story, considering that the GTI is supposed to be formed from the best and the brightest of the GTA.
So in ST:R we tried to make the GTI not only competent, but ahead of the player by several steps. Over the course of the campaign, in three places the GTI nearly wins outright. The only reasons they are prevented from doing so are bad timing in the first two instances, and the GTA rolling a miraculous save in the third. None of these can fairly be blamed on the GTI.
The EMP burst is one of those places where the GTI nearly wins. I decided that leaving the course of action up to the player would be a good way to communicate the precariousness and gravity of the situation.