Hi,
The metadata API and the "change set" feature are not "destructive" by nature. Many people think that when you copy a profile, you are copying all of the permissions for that profile, including all object and field permissions. However, this simply isn't true. While you do need to compare base profiles for a comparison of, for example, "API Enabled" or "Export Data", objects and fields are enabled separately by default, which means that you can copy just a subset of all available permissions without worrying about a complete overwrite.
It is true that you should be wary about using profiles in the Eclipse IDE, and with good reason. The plugin is "smart" and tries to only deploy changes. This means that in order to deploy a change to a field level security item, you have to modify both the profile and the custom field in order for a change to occur. This is usually a huge hassle, and so you should probably avoid doing that.
Change sets, and the metadata toolkit, however, are perfect ways to copy just the permissions you want to copy. This is because the system will only change the settings relevant to the combination of profiles and fields/objects. The Metadata Toolkit gives you the flexibility of editing raw XML files, allowing you to copy only the information you want to.
Hope this helps.