I am encountering the same issues as you Richard. I'm also in a large College and in our 2007 setup we used the same basic structure as you have described - it was good to be able to target a group of PCs at a block level and know that the sub-collections beneath would also receive the package. It gave us good scope for slowly rolling out deployments, especially in the case of large packages such as Creative Suite.
As I migrate the collections to 2012 its clear that this approach isn't going to work. I'll post in this thread once I determine a solution that looks like a good fit.