That's an interesting way to interpret Prototype. I choose to believe that Alex Mercer and the Prototype are two different entities, as in when the douchebag doctor decided to unleash Blacklight in the subway, HE died there and the Prototype or ZEUS was born. Later in the morgue Zeus woke up with Mercer's memories and thought that who he (she, it? I don't think viruses have a determined gender) was. Dr.Mercer was and always wold have been this sociopathic asshole, but Zeus could be whoever he wanted to be (literally, actually with his shape shifting and mind devouring power). Which was why Dana was confused the whole game as to why you were such a different person, you know one that would choose to save a city at expense to himself (which her actual brother would NOT do, seriously the guy was a huge, assholey ball of douche).