While Mercer as the person and the scientist who he used to be has been dead ever since before the first game began, you can still use his name for the being (aka virus) that took over his body. Half the time Mercer is referred to as either Zeus or Mercer, so both are correct when referring to it. Also, I'm pretty sure Zeus or Mercer whichever you want to call it is capable of infecting others just like Greene (or Mother if you want to call it that instead) was. Because he was essentially the protagonist in the game, he didn't do it, even going as far as to save Mercer's sister. On the other hand, Mercer when he was still alive actually did cause the initial outbreak of the virus, so in a sense he did infect others albeit indirectly.
So, as Heller was infected by the virus by Zeus/Mercer and because the thing is better known as Mercer because Zeus is a code name Blackwatch gave it, it is quite correct to call it Mercer even in Prototype 2. Heller may not even know the code name at the time of him being infected.
So in short, if you have a problem with the Zeus being also called Mercer, then you have a problem with about a third the dialogue in Protoype 1. And if we have now established it can be called Mercer, Mercer's body should be destructible by plenty of means. I mean probably even you died quite a few times in the game, you weren't completely invincible.
The bigger problem with the slogan of Prototype 2 is that it sounds cheesy, but I'm willing to give it benefit of doubt and wait how good a game it'll be.
Also, I wonder if Pariah will make an appearance in Prototype 2. A three way battle royale between Mercer, Heller and Pariah would be quite a spectacle.