If Alec has been changed so much that he will never put Julian in such a situation... Then Julian can kick back and enjoy the future.
Besides, in season three, the timeline Alec skipped out on, if we ever see it again, no longer has any Alec Saddler. Theseus has no one to fight who is saving the world wrong. In All-Star Superman, Luthor actually does it and kills Superman, it takes a while, a year even, solar radiation (overdose) poisoning... But kal has this nice speech to Luthor at the end "You've always said that if I wasn't standing in your way, that you could save the world, well I'm not standing in your way any more, in a week I'm going to be dead and buried, so why don't you just do it already, go ahead and save the world."
In the new timeline created by Alec going back to save his girlfriend... There are two Alec Saddler's unless the writers wussy out and one of them gets killed half way through the first episode of season three.
Meanwhile you have to remember that the freelancers come from a timeline where there was no Alec Saddler, but because they can navigate between timelines, it's not so much of a concern to them as they can still go home.
More so than navigating between timelines, their tech would have to have zero impact and not create alternate timelines, otherwise their travel device is counter-intuitive to their philosophy.