How to Replace Misplaced OS Files
Yes

Simply take the original installation disc that came with the Mac and re-install OSX, afterwards just do a system update to bring it up to the latest version.

When OSX is installed over an existing installation, all settings and applications are preserved, and this should resolve all issue with the OS.

However, as @Kyle pointed out in the comments, the files moved are only header files used for compiling, and should not be affecting the working OS, and since the actual OS files are not available via the Finder, highly unlikely that she copied actual system files, unless she used Terminal.

If the applications still don't work after doing this, then those specific applications needs to be re-installed individually. The above procedure will work for all applications supplied by Apple as part of the OS.