Contamination of a organisms genetics with pieces of virus DNA happens in nature ALL THE TIME. It is only because this is a GMO crop that it was tested, and found.
When the testing is finished, this may well be found to be a bit of perfectly natural, happened in the field, no-scientists-required genetic mangling.
The only difference with GM is it is done in a carefully controlled manner with a known goal, and carefully tested to determine any unwanted side effects. Random, uncontrolled genetic modification, whose consequences are totally unknowable, is completely natural.
As it is, one of the later posters linked to an article that actually looked at the research paper in question. It searched the known genomes for known toxic genomes, and found nothing. It found one possible thing that might be allergenic, looked at it further and ruled it out as well.
In the end, they found a possible cause for a GMO to be less effective - stunted growth, late flowering - and concluded that this is something that geneticists should look out for.
To finish, we have yet another study that shows how GM is completely safe. And how the media is totally untrustworthy when it comes to providing information. OH, and the article makes my point about natural virus proteins, too.