something to look at is Linotype Font Explorer. It a font management tool that’s free (they have a store included that you never have to use – no ads either). You can get it from macupdate.com.
I have 3000+ fonts with 600+ active at the moment but never any crashes like that.
You leave your system fonts where they are, don’t use Font Book and let Font Explorer manage your fonts. If you install a font with Font Explorer it doesn’t put it in the Fonts folder (which I think is the secret – only your system fonts are in the Fonts folder) but tells the system where the fonts are. Like Suitcase or Master Juggler Pro do (or did) only free.