"Disk utility" Verify permission and repair permissions
Repairing permissions won't fix a font issue. The issue isn't incorrect permissions, it's that the fonts were moved from /System/Library/Fonts/ to a subdirectory that shouldn't exist. The simple fix would be to simply move the fonts back up on level to where they should be.
If you haven't made a image then another option might be to [click click cant' think} umm it's like a alternate Reformat of the HD instead of fully wiping every thing out you only reformat and reinstall the system files (no work documents) i think I'd look that up actually.
What you were trying to describe was a Archive & Install. Which would work, but is a bit extreme, IMO, where there's perfectly suitable alternatives to be tried first.
I also don't think a mac OS X has a safe mode you see its a direct representation of Terminal (like DOS which is a command line user interface) OS X is a graphical user interface (GUI) so you see what your doing, so a mac is straight to the point no bull but windows isn't Win try to hard to be user friendly that why it has safe mode and all that jazz
OS X
does have a safe mode. If you boot holding down Shift, it will load only those kernel extensions that are needed. However, this has nothing to do with fonts, so won't help.
What you are describing there is Single User Mode. Where you boot directly into a root shell, bypassing the GUI (which is called Aqua, BTW, not "OS X")
it suck an ya might lose your job so I'd suggest you say it has probably contracted a fatal error that had nothing to do with you..
Finally, one should always take responsiblity for one's actions, not try to lie your way out of it.