Unless you converted and compiled extensions as .so files, you have to stick with Windows. But if you'll cut extra extensions (online_stats, DevConnect, etc) then i think only Utils need to be taken care of (becouse of logging functions) before starting tests with penguins on board.
There is, however, few projects which could give you some info about FOnline+Linux - Ashes of Phoenix (was running server thru wine some months back), FOnline 2 (experiments with linux server app, due to engine bug present in windows version), probably Desert Europe (but not so sure about that).