The word "engineering" is usually used for something constructive and innovative, for example, mechanical engineering, software engineering, aerospace engineering. But "social engineering" denotes something malicious, why is it so?
I suppose it's about context. 'Engineering' as a word is neither positive nor negative. In the same way, the word "crunchy' is positive when it refers to cornflakes, but negative when it refers to someone's leg!
So too, 'engineering' can be positive or negative only in context of what is being engineered. Engineering is about one person or a group of people altering something or combing things so that it/they end up in a state which better suits the engineer's needs. It is generally considered that it is ok to do this with inert matter, but not with people.
So social engineering here is negative because it is generally considered that society shouldn't be engineered.
As per Google: so·cial en·gi·neer·ing noun the application of sociological principles to specific social problems.
en·gi·neer·ing noun the action of working artfully to bring something about.
So I read this as social engineering being the artful application of sociological principles to specific social problems to bring about resolution.
In the context of your link, it is the artful application of exploiting specific social problems to bring about desired results.
A definition of engineering is: "the action of working artfully to bring something about."
The use of 'engineering' in the term 'social engineering' is merely a direct use of this definition: the actor is socially engineering. i.e. they are working artfully (and socially) to bring something about.