The original plan, if I recall correctly, was to have a longer mid-season break like they had last year, but the rest of Fox's schedule wound up being a disaster - Standoff, Vanished, and Justice were all candidates to fill in, but none did terribly well, and even the midseason shows all had...
I have a tough time believing that even on Prison Break would the conspiracy's evil plan be predicated on Pope stopping to ask that particular guy if he could use his computer.
They didn't alter his DNA, they just made sure that any existing samples were from the homeless guy they killed. Although you could still match his DNA against his sister (unless they reveal one was adopted or something)... good luck with that. You're going to need a lot more compelling proof to...