Your question rests on the understandable but incorrect assumption that slaves only began adopting surnames after emancipation or their individual freedom; for many families, this was not the case.
Although the legal naming of slaves was often entirely at the discretion of the slave owner, there is evidence that a significant number of slaves adopted their own surnames in secret, without the approval or knowledge of their masters. In the early period of slavery, these names would have usually been the family names of the men who owned them; in the later period, they were likely to be taken from male ancestors, just like in white families.
For slaves, this was an act of unity and resistance. Choosing a secret surname for themselves, even if it was the name of an owner, was a means of defying the total social control masters tried to exercise over their Human property. Adopting a common surname across an entire family or community served to foster an identity and solidarity that could not be broken easily; even if family members were sold away, they would always retain their secret surname as an connection to their wider family and as a statement of their identity.
So upon being emancipated or manumitted, many slaves would have continued to use secret surnames that they had either adopted or passed down through their families, even if the origin of that surname had long been forgotten. Those that did not have such a surname had options beyond 'Freeman' - they may have also opted for the name of a previous owner, or a name that meant something to them; certainly some opted for the surnames of the founding fathers. In any event, 'Freeman' was never in a position to become the dominant African American name in this context.
Key Source
Herbert G. Gutman, The Black Family in Slavery and Freedom, 1750 - 1925.
As a correction, the Emancipation Proclamation, enacted by Lincoln in 1863, only freed the slaves in those states that were rebelling. Because the Union only controlled some small portions of the south at the time, only a small number of slaves were immediately freed.
Slavery everywhere in the US wasn't abolished until the ratification of the 13th amendment in 1865, and there were still some slaves in the northern states who weren't freed until then.
http://en.wikipedia.org/wiki/Emancipation_Proclamation
http://en.wikipedia.org/wiki/Thirteenth_Amendment_to_the_United_States_Constitution
well one way to figure this out would be to check the 1870 census data to see if freeman was actually as common as you think. you could also compare it to the 1850 census since perhaps freeman was a more common name for pre war freed slaves
For instance this website compiled a list from the 2000 census and freeman was only 91st on that list so it seems doubtful it ever was as common as smith or jackson.