The only way to deactivate Font Book is to delete it.
I believe you're still not quite getting what A A P L is saying about suitcases. A suitcase is, as a simple explanation, a special folder that can hold many font files. A suitcase file may be named Univers, but may, and can contain a few, dozens or hundreds of fonts you can't see. An example would be "Arial Narrow" as installed by OS X. This file is a suitcase of TrueType fonts. Of which, it actually contains four fonts, which are:
Arial Narrow
Arial Narrow Bold
Arial Narrow Italic
Arial Narrow Bold Italic
Since OS X, it has been very difficult to open these suitcase files. But in OS 9 and earlier, it was very easy. People, and lazy designers (as A A P L mentioned) routinely put all kinds of unrelated fonts into a single suitcase. So loading a suitcase named Copperplate could easily also contain Helvetica, Symbol, Courier and any number of other fonts that will conflict with fonts in the System folder.
As far as I know, Suitcase Fusion is the only font manager that will not only show you what fonts are grouped inside a suitcase, but also let you enable only the ones you want. With all other managers, including all previous versions of Suitcase, you can only activate the whole thing. So if there are any conflicting fonts within a suitcase, you can't avoid opening them.