The means to an end are actually very very important if you want to consider an action overall evil or good.
I want to create world piece, a good goal isnīt it?
therefore I kill every human being on earth to achieve it
This is one of the most extreme examples but still to illustrate that means are of importance it is valid
As for the example of the bbeg, it could very well be that he sees the errors of his way when confronted with the heroes and if spared by the heroes after foiling his plans atones and becomes one of the major forces of good in the universe...
an unlikely scenario but still a possibility denied by the sneaking murderer.