I thought the idea of safe mode was to protect sites like MtGox from losing everyone’s entire balances in the event of a catastrophic exploit. Safe mode shuts down their transaction processing until they can work out what’s going on, and upgrade/patch if necessary.
For the sake of appearances, it’s better not to have safe mode turned on by default (because “remote tampering” of one’s software is not popular with many people). But why not have safe mode disabled by default, and provide an “-enablesafemode” switch for those who want it?
Previous discussion was here: Development of alert system and here: Version 0.3.11 with upgrade alerts