Being president does not mean being in total control, but it does mean being an effective manager. An effective manager trusts his subordinates to carry out his agenda. The question that requires an answer: Does Lincoln's lack of reaction to the abuses within his government and military a tacit implication of approval?
First, Lincoln did react to overabuse by Fremont by relieving him.
Second, no one claimed all of Lincoln's actions were perfect are not subject to criticism.
They are looked at on balance.
Davis's record on protecting civil rights was no better then Lincoln's.
The fact that in the midst of a bloody civil war, we were able to have most of the nation remain under civil law and not military and to have elections, says a great deal for the Consitution, its checks and balances, and Lincoln's respect for it.