Welcome jsides !
I split your post off from the longer thread because I think it deserves its own discussion. The question is a very good one !
Now, this is just my personal opinion, and remember this is coming from a proponent of using 301's.
In your situation here's the way I would look at it.
If your mainsite.org/littlesite/ can stand on its own two feet, meaning it's not simply duplication of other content on mainsite.org, I would simply split off the littlesite.org to its own domain name and remove the current mainsite.org/littlesite folder. Linking instead to the new domain.
In my mind it all depends upon exactly how closely related the sites/content is going to be. If you can do it all on one site, do it on one site. However if there is a driving reason behind having a second domain, such as the Branding purposes you describe, that's one of the very valid reasons for multiple domains.
So that's my take on the base question.
As to how this will affect PR/Link Popularity, what you're doing basically is creating twice as much work for yourself on the link building side of things. Plus you're likely doubling your hosting costs, creating more work/expense to have a second site designed and kept up. Etc.
Those are all reasons why you normally wouldn't
want separate sites and instead use a 301 to redirect all of the umph you can to a single location.
However in your case, with the Branding implications especially, I think it's worth the extra work and expense.