The whole purpose of Syncronisation is that any changes made on either device get's applied, so if you're on the road and someone gives you a different phonenumber, you can add it to your phone and when you sync, the new number updates on your computer... It's a two-way transfer.
If you Do want to only Sync one way, you'll have to select Reset All Devices... from the Devices Menu. This will completely overwrite all entries in your phone with the entries in your computer. It will also reset the logs of changes so any new changes will be applied next time you sync.
If your Data is getting corrupted when you Sync, there must be Bug in iSync. Report it to Apple using Provide iSync Feedback from the iSync Menu.