Honestly the more I read and think about it the more I think Darkness isn't actually the bad guy here. Something that has been bothering me, why does darkness react so strongly with protection? When people want to protect others that's when we tend to see people most easily be consumed by their own darkness. When things fall into sleep the darkness tries to protect them, an entire species of creatures called the dream eaters exists in two forms one to keep sleep going forever the other to protect the sleeper. As said a couple times in this series sleep is often equated to protection, a type of safety where you are alone but shielded from the outside. Even in DDD when Ansem the Wise recounts the hearts that fell into the darkness of Sora's heart he says that some were trapped there but others were welcomed into its warmth. For such a vicious force darkness gets associated with warmth, protection, security, etc....
So now what about Darkness? Well think about the keyblade war according to legend it all began when people of the light grew greedy for kingdom hearts and began to fight over it and then darkness was born in their hearts. The MoM said the original keyblade war was fought between people of the light and beings of darkness which makes it sound like a battle of good and evil, yet according to the legend the entire fight began from greed. So what if darkness is nature's defense mechanism. What if the people of the light were the greedy and evil ones, of which MoM is the last of, and the darkness was born to stop them. What if the original events went something like this...
People of the light greedy for the light fought over kingdom hearts and in the process they shattered the X-blade, the counterpart to kingdom hearts which exists to safeguard it. The blade split into two halves, light and darkness, and further into 7 lights and 13 darknesses. Maybe that's where Darkness first truly came from. The original Darknesses might have been the 13 hearts of darkness that came from the X-blade, and they still retain their desire/purpose to protect kingdom hearts from the greedy people of light. Likewise maybe the 7 lights are also retained a desire to protect but manifested that in a different way, as long as they exist they prevent light from vanishing. In essence it's a two prong defense one keeps light from vanishes the other seeks to take out any who would claim the light for themselves.
We don't know how the war ended up but in the end I think maybe Darkness won, they stopped the light from taking Kingdom Hearts and peace was brought to the world. But the darkness is unbalanced it didn't stop with the war, it continued to infect and spread silently, swallowing and imprisoning all the light it could not for evil but to protect it. So it's a slow growing plague and yes that makes it a negative but in a sense that also means it's the security system. As long as it exists kingdom hearts is lost and the world is on a course for destruction, but at the same time kingdom hearts is out of the reach of those who would abuse it and the 7 pure lights ensure the world will never truly cease to be. It's a broken messed up balance but a balance none the less, one which protects kingdom hearts from greedy people.
Thus the MoM trying to destroy darkness may not be a beneficial thing. On one hand he be taking out this plague that has kept the world in a cycle of destruction but on the other hand if this is nature's way of protecting kingdom hearts then he's removing the obstacles that stopped the people of light from claiming kingdom hearts in the very first war. In other words he might want to destroy the security system not because it's a broken messed up system, but because its still functional enough that it blocks his way to the prize. Darkness may be an antagonistic force but the MoM is the real threat and destroying Darkness would just remove the barricade in his way.