I suspect that doing things to traffic lights wouldn't change the traffic flows much, when Gridlink is controlling the flow of the vast majority of the traffic (If this anywhere that has banned manual controls they might have gotten rid of traffic lights entirely).
Let's say you are are traveling along Avenue A, coming up to the corner with 1st Street, and there is a traffic light there which is currently red for you. Hacking the traffic light to turn green for Avenue A and red for 1st street does NOT stop Gridguide from sending traffic from 1st street through the intersection (and keeping traffic on Avenue A stopped). As far as Grid Guide is concerned, the light hasn't changed (it didn't tell it to do so). So you may still have trouble getting through, depending on the traffic levels and if you are under manual control or not.
Now, if you just passed through and want to stop pursuers, hacking the light to mess up traffic (perhaps an accident, perhaps just confused traffic slowing things down), then hacking the light without hacking the host might be fine. But if you want to give yourself true fast travel, you'll need to hack the files on the host to tell it that (for some reason) it should keep giving priority to Avenue A through all intersections (probably setting a file to emergency responder mode, or something like that).