I think it is inaccurate to depict Rawlings' revolutionary actions against certain members of society as being targeted towards Akans. At best, it is circumstantial evidence since it is unlikely that Rawlings, who is married to a prominent Akan, will bite the hand that literally feeds him.
If anything, it is better explained by the fact that "Akans" have traditionally controlled the resources of a large sector of the modern Ghanaian state. Consequently, the revolutionary fervor fell upon Akans (wealthy, intellectual) because they represented that class of society which in Rawlings' opinion was the root of Ghana's evils. If some section of the NDC questions Atta-Mills' ambitions to lead the party in 2008 it is because he represents more the "Professor" than a man of the people. It is not his failure to lead the party to victory (in that case Kufuor was similarly disqualified--he failed at least twice in his bid for the presidency: first against Adu-Boahen, and then against Rawlings).
If you dig into the historical record you will find that non-Akan members of this "oppressive" class were similarly "persecuted". The NPP (Busia-Danquah) tradition still largely represents this wealthy/intellectual class. On the other hand, the NDC says it represents the under-privileged of society, and in the last election we saw some further refinement of this political philosophy. So that when the Cape Coast municipality decidedly votes against the NDC, it is better understood as a class reaction rather than a tribalistic one. The interests of the wealthy/intellectual are better secured when the NPP is in power because the NPP tradition is sympathetic to them. On the other hand, the (P)NDC has not particularly paid attention to wealth/academic qualifications except when it served practical purposes.
You are right when you mention that Atta-Mills appeal to the NDC was that he sought to bring some respect for intellectual contributions into the NDC.
We must be careful when drawing lines. In the NDC as well as the NPP, it is the "Akan" class which stil wields power. On the ground, people choose what they believe will best serve their interests which is why Rawlings is still widely popular among many of the rural and urban poor and equally unpopular among the wealthy/intellectual class.