In many cases direct genetic modification is *less* intrusive than other techniques of creating more suitable species of plants...the non-GMO method generally involves forcing random mutations via chemicals/radiation and then selecting for the traits you want. Of course there may be a bunch of other mutations that you didn't select for/against that could cause problems in people.
However, we do not know what long-term unintended consequences there may be to this type of gene modification, because there has been no long term. While selective breeding of natural mutations -- even of a relatively "forced" variety -- has been around for millennia.
The point being that one method is time-tested and the other one not. We don't have any long-term examples of jellyfish genes crossed with plant genes. We do have evidence that bacterial and viral genes have invaded other organisms, but again those we have evidence of were very long ago and have had eons to weed out any bad variants or effects.
I do agree, however, that the regulatory system is faulty.