First of all I want to address your last sentences (even if it might not have been seriously): We are a long-running beta that falls exactly into the category of "won't be closed, but won't graduate either". See Graduation, site closure, and a clearer outlook on the health of SE sites. Seeding questions doesn't make any significant difference. We should really not base decisions about single questions on our question rate. It is a different story for scope questions, where establishing new topics can lead to sustained and significant increase due to recruiting new users. As you yourself analyzed pointedly: Our problem is too few users:
The top 10 most active users wrote 890 questions and 1684 answers for
26% of the questions and 20% of the answers.
But I digress, I just felt a strong need to promote quality before quantity. So lets get back to separating pros and cons:
If there is a good reason as in this night question, it is absolutely fine to ask for one side (side as in either pros or cons). This is probably true for question that are heavily biased towards one side. In that case it makes sense to ask about aspects of the other, less prominent side. Other than that, I can't think of reasons to separate. Very often it isn't meaningful to strictly divide, as there is no clear line between pros and cons. One aspect might be an advantage in some respects, but a disadvantage in others.
So in general I don't think pros and cons should be separated. And to have a real discussions about the pros and cons of separating pros and cons, I would need to have concrete examples or characteristics of such a question.