Hi Jessie,
I don't have SFDC, so I can't comment on anything from that regard... but I will tell you that I've used programs sparingly thus far within my engagement program.
It's set up with a folder for General, Early, Mid, Late and Oppty Mgmt (our streams) and then I use a number/naming convention to keep things in order, i.e. 1a - [Email 1], 1b - [Landing Page 1], and so on and so forth.
We have some instances where I want to hyper segment our content by industry, location and job title. For this, I use a program so that I can dictate who receives which email and what version of that email to accomplish all of this segmentation. I also have a program for one of my organization's whitepapers. Technically, this progam "lives" in our website assets area (just a general, top-level folder where we store standalone landing pages and forms for our top assets) and I've just dropped it into the nurture stream from there.
Looking back, I'm glad I handled the whitepaper and similar assets this way even before the Engagement Engine because now my organization is set up to use the "send once" functionality where Marketo will skip an asset if the person has already received it.
Final thing - I know you said that your main consideration for sticking with programs is for the progression statuses to sync to SFDC. I can't say anything to the pros and cons of that, however, for our progression statuses, we're really just looking at lead score in the Engagement Program. I thought about getting granular with the progression statuses (In program, opened email 1, ct email 1, etc.) but that would quickyl devolve into a nightmare. I think it's best to stick with a simple, In Program, Engaged, Success, or whatever Marketo's recommended progression statuses are. Really, knowing they opened email 1 is not that useful, especially for your sales team. It's best for them to take a moment, glance at the lead's activity log and get a quick overview of what the lead has done and what items they've been interested in. At least, that's my two sense and how we are working with our inside sales team.
Hope this helps - I'm interested to see what other people have to say!