I think it is fair to say that each of us in our given professions (mine being law) ought to avoid being a proximate cause of something deemed wrong even though technically legal (for example, I would not be a "mob lawyer" even though there are some technically very good lawyers who do that work). But even here that is an individual choice for each actor to make. For engineers, some may see it as a great opportunity to do advanced work in some of the social media companies while others may regard such companies as being engaged in unethical conduct as they at least sometimes use dubious techniques to try corral us as consumers into their tight little worlds. For any given engineer, working for such a company doing such things is a matter of conscience. Some may say yes, others no. The same is true in working for a defense contractor or for the government. Or for any other work that is legal but ethically suspect in the eyes of some but not others. It is your choice and it is your conscience.
The author of this piece reflects what I call the bane of associational thinking. He uses the royal "we" to define a group (here, engineers) and then prescribes very broad goals for what "we" "ought" to do. Since all the things described now stand as a matter of private choice over which the "we" group as a whole has no say, then the only way to translate this sort of thing into practical action is to form formal associations, assign things to committees, and then issue a series of prescriptions on what the group members ought to do. That may be fine in terms of the association giving rules that amount to exhortations to do good (who would disagree with that). But, beyond that, do you really want an organized association dictating what today stand as your private choices for your career? Or, worse, do you want such an association to lobby governments to adopt their strictures and give them the force of law? I would think not. How, then, can "we" do better? Of course, the question is always described as difficult and is left for further discussion precisely because it has no real answer apart from acting on individual conscience or apart from the potentially coercive ones of letting some association or government dictate your career choices and opportunities. Perhaps this sort of reasoning is justified as encouraging people to have a heightened conscience about what they do, and in that respect it is fine. But that is really as far as it goes before veering into unacceptable alternatives.
Our capacity to do wrong is innate to our nature, as is our capacity to do good. We should not stop trying to do good through our creativity just because others can take what we do and commit wrongs with it. Nor should we feel guilty about what we do as long as we in good conscience can say to ourselves that we are doing something productive and worthwhile and not directly causing harm to others. The "we" issue is in reality much more of an "I" issue and, for that, you should examine what you do carefully and strive for the good regardless of what others may do with it. If you want to exhort others to do better by your standards, then all the better. Just don't dictate to them on matters over which people in good conscience may disagree.