You'll have to back up your bookmarks and restore them, I'm afraid. We can't issue DROP TABLE or whatever kinds of SQL requests as that will be a deallocation of clusters without a sanitation of the cluster.
Best I can tell (others please verify for yourself), in FF 3 when you back up bookmarks via FF menu options, it backs up only the bookmarks out of the places.sqlite file to a "bookmarks***.json" file, and doesn't BU the browsing history in the places.sqlite file.
For those interested, there is a Firefox (3) extension, "SQLITE MANAGER" that views .sqlite files. There are also numerous .json file viewers.
Didn't know .json files could be read w/ text editors.
What you mentioned seems like a simple way to go. I'm curious (rhetorical question) why Moz decided to combine the bookmarks & history in one file, even though they give a way to "delete private" including history, albeit not securely.