This is a great discussion! I am trying to wrap my head around your campaign layout, this is intense for a Thursday night.
I think that option 2 makes sense if you want to easily track the performance of content. Option 2 makes sense if you are trying to tightly track the performance of the publication.
Which is the most important to you? You can still track either, but what is your primary goal for this initiative, measuring content performance or measuring publication performance?
Are the publications other websites? I may be over my head on this, but I would go for 2. In my mind, the publications are referral partners/sources.
I am curious what the Champions Josh and Charlie think here. Jeff Shearer led a talk on using centralized content programs. Check out item #8 here:
http://www.jeffrshearer.com/15-marketo-protips-advice-you-can-implement-today/ and his talk from summit.