Because if momentum isn't conserved, then all the neurons in his brain will stop firing. It would literally give him brain death.
That's a misconception -- as is your post about blood stopping. The blood circulation system is a closed pump system -- it is virtually unaffected by external velocities and can only be affected by the most extreme of accelerations (and even then, it should recover as long as no damage was made to the heart or main arteries). The only reasonable thing that could affect the blood supply circulating would be a stoppage of the heart, which now gets us to the brain. The brain is not a mechanical entity -- that is to say there are no moving parts except electric signals, and these electric signals move along very defined paths. That is to say that a brain is similar to a phone. You can do all sorts of things to a phone and it will still work fine because the electric signals on the chip inside have very defined paths. You can travel in a car with a phone and come to extreme stops when an asshole hits the brakes in front of you and the phone will continue to function billions of times a second in clockwork precision as if nothing had happened (as too does your brain).
The only thing I could give you as a plausible reason for momentum loss killing Freeman would be if the momentum was lost nearly instantaneously, which would impart an enormous acceleration on poor Gordon and maybe rip an artery out of his heart. However, there are ways to escape this conclusion, such that it is not true that there are no imaginable scenarios in which Gordon could survive:
1. Teleportation invokes relativistic effects which causes simultaneity to go out the window, such that teleportation does not actually happen instantaneously for the object (or person) being teleported, though it may appear so to any scientist or observer witnessing the object (or person) being teleported. This would allow for a very gradual removal of momentum, thereby causing absolutely zero harm to the teleportee.
2. Teleportation causes a blackout of Gordon's brain during the process (this makes particular sense if you imagine that his brain is disassembled and reassembled), such that the process may actually take many seconds or longer, giving his body plenty of time for a gradual loss of kinetic energy.
