Many Presidents of unsettled countries see their own military forces as the primary threat to their administrations, and try to counteract that threat by promoting officers and organizing forces on the basis of loyalty rather than competence. That works well enough until you actually have to fight somebody, as the late Saddam Hussein, among others, learned the hard way.
There is no military force in Africa that can challenge the Nigeria Army on its home territory. (Egypt and South Africa may have better Militaries but they lack expeditionary capabilities).

No Western power is likely to intervene militarily in Nigeria in the foreseeable future. Nigeria is beyond the capacity of the British and French militaries (logistics, boots on the ground, simple financial costs, post-conflict stabilisation operations) , so that leaves us with the US.

So a Nigerian president (and one with a PhD for that matter) will be smart enough to know that a coup or an insurrection is more likely than an invasion and the having loyalists around is a wise course of action.

No one is suggesting that these officers are not competent because they are Christian or from the South. Nigeria has been ruled for most of its independence by Northern generals, so when Obasanjo "depoliticised" the army purging it of officers who had previously held political appointments, many Northerners were affected. The less political and hence more professional army officers tended to be either from the South or Christian, so the president has a lot of names to play around with.