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Tags merging has been the traditional calibre behaviour, it was just that such behaviour got "broken" with calibre 0.8 changes. It was me that requested Kovid restore the original behaviour. The reason is that many people like myself put their own values into the tags field, like indicating wish list items, books they have read etc. Having your own tags overwritten when the tags column was the "traditional" approach to storing extra information about your books was too destructive and dangerous. Particularly if say you were doing a metadata download to update some other fields and had forgotten you had the tags column ticked. There is no undo feature in calibre, and to accidentally lose sometimes important information by overwriting for many users is not the right thing to be doing IMHO.
I did suggest to Kovid the option of a controllable setting but he chose to just fix the behaviour. There is no way to change it back to overwriting. However I would suggest that should rarely be a problem? As if you are adding new books they should not have tags to overwrite. If you are cleaning up your library and your books have tags that you want to replace with a metadata download, just select them, hit E and tick the Remove all tags checkbox.
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