Horror sequels are always about topping their predecessors (unless they're DTV, of course). Doing things bigger, better, scarier. So, if Telltale were to top killing off the PC at the end of S1, how would they go about doing it?
By killing off the PC in mid-episode.
Why not? A lot of shit went down in part 3, where most of the original group was slaughtered. How else could Telltale up the ante besides axing the PC before part 3 is even over? Player control would then abruptly switch to another character in the group, and maybe it could even be a character Telltale has gone out of its way to make us hate, just to twist the knife.
Looking at the pattern of the game's story arcs so far, and the WALKING DEAD universe's one and only real rule - "anyone can get it any time" - don't be surprised if this comes to pass.