The government decided to promote western migration during the Civil War because President Lincoln feared that a Union would not agree on the matter.
So he facilitated migration to the west by promoting the concept of free soil, so white settlers would populate the region with allies that opposed slavery. This would also make the matter easier to solve because this people would refuse the expansion of slavery.
Congress then passed the Homestead Act and the Pacific Railway of 1862, which helped with the westward expansion.