you could delete the meta tags from the include then go into each page an manually add them.
If the Include contains the entire <head> element, wouldn't it then be too late to add anything?
I hope this isn't the case, because then the include would have to, er, include a dynamic element to give each page a different title. And then you're in developer territory.
If you're only including the content of the header, you can delete the unwanted <meta> from the include file and put it into each page separately. How many pages are we talking about? I don't think g### would be real thrilled about batches of pages all having the identical meta description, for example. (Was going to say meta keywords, but I think they've simply stopped reading those.)