Urm.... No he didn't, that's the point! Franklin could still use his powers. The X-Gene wasn't touched, not really sure what is difficult about this concept.
So in your opinion you're past should dictate your future? If that's the case I can't wait for the bell to toll for the X-crowd for all the messed up things they've done.
We seem to have very different ideas of what genetic manipulation is. In my mind if Reed rewrote his son's DNA to make it invisible to Krakoan tech then yes that is genetic manipulation. However that isn't what happened. So instead of talking it out with Reed, who has to be one of the most reasonable people in the MU, Charles and Eric act as judge, jury and executioner for a pre-crime. Their actions were morally wrong and foolish. Reed Richards isn't the only super genius in the MU and making an enemy out of a friend was a dumb move. I can't wait for all the evil super geniuses to have the same idea and do the exact same thing Reed did. You can't stop progress.
Make peace not war! If the mutant nation of Krakoa want to turn not only the supervillain community, but the superhero community into enemies so be it!. We can all sit back and watch the mutants get decimated!