After using fake charger with my Macbook Pro Retina 13, an original new one won't light up
Sounds like a DC-In board or logic board issue. It could be possible that the fake one cooked the parts of the logic board which provide the onewire communication between the SMC and adapter. Before you go replacing parts, make sure the contacts are clean on both the rMBP and MS2 adapter. Ensure no pins are pushed in and stuck on the adapter. Also ensure that the DC-In board did not get pushed in.

If it is new enough, it should still be covered under AppleCare, and you can take it into a ACSP for them to take a look at. Don't mention any fake charger should you take it in for service. If you're lucky, it's just a DC board, so here's hoping.

Sorry I can't provide much more help, it's hard to diagnose HW problems without having the machine in front of me with known-good parts to swap and test.