I think Regina knows exactly who Emma is. But Lana has mentioned several times in articles that she is very aware that Regina does love Henry – so if that is the case, there is no way that she is going to kill Emma because she knows that Henry was so intent on finding his birth mother (from a mortal perspective), and because she knows that Henry believes that she is the EQ from a FTL perspective. What mother wants their kid to think they are an EQ – even if they are??? So I think the last thing she is going to do, simply because of Henry, is to directly do away with Emma. I think that instead she just wants to let the curse run its course and try to hurt MM as much as she can before whatever effect Emma is going to have takes over. I actually think Regina feels more threatened by Emma because of Henry then because of the curse – not simply because she is his birth mother but because deep down she doesn’t really believe she has the ability to truely love someone – so I think she fears that people will figure out that she isn’t fit to be a mother and that somehow Emma will be able to take Henry away (Archie has even hinted about this). (Although in the real world a birth mother who suddenly showed up 10 years later with Emma’s history would never be able to get Henry!!).