Then you risk having two copies...
Scan you, destroy the original, transmit scan data, reassemble you at the other end. That's the only way to be sure... and would explain all the "transporter accidents"
EMP does not equal CME
No... but a big CME, as it interacts with the Earth's magnetosphere, can generate an EMP. That's what actually causes the overload in electrical systems, not the charged particles.
Cyborgs are just kinds of humans
It's conceivable that something could cause a knee jerk reaction and suddenly a bill appears suggesting people with brain enhancing modifications are no longer "people". Then all your inalienable rights go out the window. Perhaps a law is passed saying modified humans are no longer human and therefor no longer citizens. Again, your rights go away. It's something that should (eventually) be addressed before stupidity happens.
While a person is smart and can make rational decisions, sometimes people become dumb, panicky, dangerous animals.