They can easily accomplish this through Flash - I was hoping they were going to do something about that, especially with how S1 of Flash ended. Barry should have saved his mom and it could have changed things in the universe -affecting both Flash and Arrow.
Heck, they could easily accomplish this with the lighter changes Barry made (by traveling back, such as saving Cisco, or going back to S1 to find the secret of gaining more speed...."time booms" that ended up affecting Arrow). Just change things around.