You're over thinking the time travel thing. Clark and Michael will obviously be returned to the present at the time they left, again I'm pretty sure the show displayed this before with the ring's time travel capability along with when Brainy pushed Clark through time I believe in "Homecoming"...Rokk is referring to future events that have already happened. Remember when the three of them first time travelled back to "Smallville" they thought something had happened because Clark wasn't Superman yet and Garth nearly revealed his superhero name to Clark and had Rokk clamp his mouth shut.
All of Clark's history has already unfolded naturally by the time we've reached the Legion timeline. We know this already from the the original founders first trip back to the past. Nothing has been disrupted in terms of that.