And we don't get to see any of what I'm talking about because of reasons I'm only just realizing don't make any sense.
The car crashes, Lee passes out in the woods, wakes up, and the place is swarming with zombies. He comes upon Clementine and it seems like this has been going on a bit, same with the farm, meanwhile in Macon it's like it's day one. If things were so far along already, it should've been affecting stuff to a point where Lee's convict situation wasn't an immediate priority, or at least would be something they're aware of. The emergency vehicles heading the other way seem more like the beginning, not well into it like the amount of walking dead would suggest.
I know it's a video game, but that sequence of events with the setting doesn't make add up. Didn't realize it until now though.
Well... Lee was a convicted murderer. It's entirely plausible that transporting him away from somewhere that wasn't about to get overrun (which he could use to escape) was viewed as a priority or that it happened because the police/government had viewed the initial reports as something they could contain. You need to remember that at this stage, people didn't know that the infection was present in everyone... they thought it was just done by bites. They probably under estimated the severity of the situation... it's not like the CDC could make heads or tails of it until after it was too late to get the word out. Once the people with infected bites/other serious health concerns showed up in the refugee camps, it was all over.
As for Macon... Macon is a city of about 231k people in 250 square miles that doesn't get major traffic except people trying to get to Atlanta or Savannah. This means the outbreak would have moved more slowly because Macon is less densely packed than Atlanta (about 5 mil in 132 square miles) or Savannah (372k in 108 square miles), which basically fell overnight because of their population density and refugees/escapees. Basically, people were leaving Macon to get help, not going to it. As such, it would have been less devastated by the outbreak, at least for a time. This would also help to explain why they were moving Lee: the city in which he has been tried wasn't being as affected as another and people hadn't been taking it seriously yet.
As for Clem... she had probably been hiding out for hours or a few days at most. It's not like she was getting food or supplies or anything... she literally hid in her treehouse when her babysitter turned. She hadn't left the backyard. Considering how long it takes for a bite to kill (hours), it's likely her sitter was bit before she showed up or before the state of emergency was declared.
I'd also like to point out that the government would be very slow to react to an outbreak that was 100% lethal but had "people" walking around still. You can't just go gunning people down if they might be infected; people have rights. You have to suspend those rights and declare a state of martial law in order to pull it off without the general population trying to fight off the government forces gunning down their neighbors. It also takes a lot of effort to keep a quarantine, especially when you have injured people coming to you for aid and hiding their bites. You can't hold a line like that without just gunning down anyone that approaches. It's a Catch-22: ether you cause a state of panic to contain an outbreak or the outbreak causes a state of panic when it breaks out.
tl;dr - The scenario makes sense within the rules as established by the greater source material, but the entire thing hinges on the government not burning down entire cities to contain the outbreak... which we would probably do in a heartbeat, even if it would end the legitimacy of the U.S. Government.