1. "He changed the rules" According to the theory, in Ben's original timeline, Alex didn't die. When Widmore's men killed Alex, they altered the events that had happened in Ben's original timeline. Ben was completely shocked because he didn't think that Alex could die in the new timeline, given she survived in the original timeline. Thus, he has to balance the universe by trying to make up for her death: Killing Penny.
Three new observations from Season 4:
2. Sayid is working for Ben because Ben has promised Sayid a second chance with Nadia in exchange, Sayid would help Ben course correct the new timeline off the island to preserve events from the original timeline. Once they clean up the events in the new timeline, they would get safe passage back to the island and access to the time machine, thus allowing them to travel back to 1996.
3. The smoke monster killed the mercenaries because in Ben's original timeline, the mercenaries had never come to the island. When Ben locked himself in that "back room" he was doing something, alerting someone, to the fact that these new people could potentially alter the new timeline. He knew this would indirectly bring the smoke monster, the course corrector, to eliminate the people who didn't belong.