Board Thread:The Panopticon/@comment-1711089-20140322010838/@comment-207.181.249.206-20140607183237

Also Clara DOES ask the Timelords to help change the future when spoke through the crack to them. If she had met the 12th Doctor when she went into the Doctor's timeline, she would likely not have said that.

But I guess I may have also answered my question about what caused the Alternate Timeline. This break could actually be an instance of Parallel Universes rather than an Alternate Timeline. Since the Timelords have narrative-God-like abilities, they could have allowed for Parallel Universes here instead of an Alternate Timeline, allowing a Parallel Universe to bleed through to the Universe that we're watching to allow the desired end result to have occurred.