So maybe I missed something crucial along the way, but was it ever stated if Ethan was in the early process of getting infected and actually had some degree of the virus during the events of the game? Reason I ask is because having watched gameplay online, I didn't get the moment after the dinner scene where Ethan's foot gets cut off should Jack attack you and Ethan can somehow reconnect it very easily with first aid. Could that be why his hand was also seemingly reconnected without worrying about muscle/nerves/bones etc? Maybe that's just bullshit Capcom writing, but then again given the December demo had the player-character get infected at the end should you get hit by the Molded - and the fact Ethan shows no signs of infection after taking damage from said creatures - I'm more inclined to believe he had somehow benefited from Eveline's virus minus the negative symptoms that came with it.
I'm also leaning more towards the argument Ethan is/was in fact an Umbrella agent/employee sent to either investigate his partner's disappearance or possibly cover the whole thing up. Whether or not Mia is part of Umbrella or a rival company altogether is another thing. His ease of use with weapons also tends to suggest he's been trained with firearms; I also like the idea that he pretended to be scared/innocent/desperate to the Deputy so as to not blow his cover.
All just speculation and as stated could very well just be plot-holes in Capcom writing, but this has indeed been one of the better post-game debates I like having about the lore and whatnot.