I think a little clarification is in order:
1) Apple does not ship Macs from the factory with the full MS Office installed. (there are special circumstances when you order in large volumes and provide your own image). However, they do ship with the Office 2008 Trial. This is a time-limited trial.
2) As stated, Office 2007 is for Windows only. Office 2008 is for Macs (only). This is usually how the MS Office releases go.
3) The migration assistant does not wipe out any applications. Unless you have removed them, they are still there. In the case of MS Office it might be that Office 2004 is being preferred to the trial version. This is actually a good thing in my book.
4) With very few exceptions everything that came on your computer is on the restore disk, and the "extra" applications can usually be re-installed without wiping out the os. There have been some some extra files (like songs) at some points along the way, but I don't think that that has been the case for a while.