I assume that you are asking why the federal government helped to suppress the rebellion. If so, the answer is that slavery was completely legal in 1831, which was when Turner's rebellion happened. The federal government did not prohibit slavery in any existing states, though it had specified (in the Missouri Compromise) which territories could and could not have slavery.
In 1831, a slave living in a slave state was legally the property of his or her owner. Slavery was, in states where it was legal, just as legal as owning a horse or a cow. Because of this, it is not surprising that the federal government would help to put down a slave rebellion. After all, the government was simply helping to uphold the law.
Slavery was completely legal in Virginia and many other states. The federal government had no position on the legality of slavery in 1831 except for the fact that it accepted the laws of the various states on the issue.