I definitely understand the need to keep a clean tree of bookmarks.
I'd say that the solution isn't to store low priority bookmarks outside the tree, the solution is to move away from the tree paradigm. Let me introduce you to tagging
Wait, you say! Neither IE nor firefox can do tags, everyone knows they store bookmarks in a tree!
Download the Yahoo version of the Firefox delicious add-on (there is a 2nd out there that is not as good). Install it and set up an account. Then install this great plugin on all your computers, you can now share your bookmarks, even access them from other computers via the delicious site! So what to do if you use IE? Switch to firefox
Since you can search easily now, it doesn't matter if you have a million bookmarks (Im halfway there already, I think). Want to keep things clean? Add a "tmp" tag to the temp ones, then you can easily find them all and just delete them.
So this is the way I've dealt with my bookmarking needs, both long term and temporary. It works pretty well.
Btw, the delicious add-on can be set up to automatically to not share your bookmarks if you want more privacy, however keep in mind that they are still on a 3rd party server.