A few points:
1) The assumption that smashing someone in the head with a baseball bat doesn't destroy the brain doesn't make much sense. That's the whole reason getting smashed in the head with a baseball bat would kill you, is because that impact did enough damage to your brain that it didn't function anymore. The series uses melee weapons to the head as a fairly regular way to kill walkers.
...however, I'd point out that that's not relevant as well...because:
2) The virus doesn't kill. They all have it already. The virus only reanimates the nervous system of the dead, which has a tendency to rot pretty nastily, meaning you get a heck of a bacterial infection that kills you if you get bitten/scratched by walker (and presumably if you eat a nasty rotted one). Anything that stopped that bacterial growth (like we already do with butchered corpses of animals) would stop that meat from being dangerous, as the virus itself is not a danger to those that have it/contract it...only a danger to those that happen to be around them when it reanimates their dead body.
Yes, there are issues with this (Why are newly created walkers just as deadly as ones that have been rotting for a month? Why does getting walker gunk in your eyes not get you as infected as getting it in a scratch?) But these are the mechanisms of the story nonetheless, and those mechanisms would not make someone that ate properly cared for/cooked meat that happens to be infected with the same virus they already have anyway die from it.