I don't think there is currently a workaround. But we discussed several times that this should be an option during download. So that Galaxy attaches the metadata to the file. Any contributions welcome - for example where would you put such an option?
in my opinion the header belongs to the data and it's no question that the data gets of course saved together with its header. Usually all downstream processing tools and functions should be able to handle a header line.
So, I think there is no option necessary to include or exclude header data. After the download it should be up to the user what to do with the header data.
An automatical inclusion of the header in the data download in Galaxy would be nice. ;)