One major issue you are running into here is CS3 was made for a much older version of mac. ( leopard 10.5.4)
However it should be able to install. And you are correct, we definitely need to reinstall from the disks, or from a download.
But first, we need to install this Java update. http://support.apple.com/kb/dl1572
Once installed, next if you have the in stall disks lets use those to reinstall indesign.
If you do not have the install disks, you can re-download either the CS3 suite you purchased, or you can download just indesign CS3 if you purchased it separately, and you can download it from this link specifically.
You will need your serial number for indesign, if you dont have it let me know.
Let me know if you get stuck at any point during the download or install process so I can assist you further. And if all goes well please remember to reply here so we can mark this question as resolved with a 5 star rating!
Senior Technician and Network Switching Systems Operator / Maintainer.