How do I disable auto-sync in HTC Sync 3.3?
According to the download page of HTC Sync Manager, HTC Desire phones should be supported.

In my case when I first started the application it started loading all my media files from my pc (which took some time). After everything was loaded, the music etc was stored in my Media gallery of the HTC Sync Manager.

If you want to disable the synchronisation of your phone on connect, disable the option "Automatically start sync when device is connected" under the More tab. In my case that tab was only available when you connect your phone (probably to be able to use different settings for multiple phones).

So maybe you should just try to reinstall the latest HTC Sync Manager, because it should work for your phone too. Just be a little patient.