In terms of being certain that all the scholars on the ship were wiped out, completely obliterating it is the best result. Any other method could not be as quick or certain. It all depends on what your objective really is : Making sure all scholars are wiped out vs Wiping out as many scholars as possible while minimizing collateral damage. Akainu seemed to realize that the 1st objective was probably more important to the WG in that situation.
There are probably other methods to deal with low morale amongst troops, but I only saw Akainu do something about it. Did Aokiji even recognize the issue and try something like rallying his troops and instill some confidence in them? Even then, I still think Akainu's method is more effective. Even extremely demoralized troops will stand and fight when they know that running is not an option. A soldier who is surrounded and fighting to the death will do alot more damage than a soldier with doubts and an avenue of escape.
His nature does not mean he is stupid or would make a bad leader. I still see him making plenty of decisions that help the marines accomplish their overall objectives, even if the means are ruthless.