I can think of two ways I'd consider worth trying.
One way is using PDFsharp to call AddPage() for each new page and draw a rectangle in the color you like before calling RenderPage() to draw the MigraDoc content.
Here's a sample that draws nine MigraDoc pages in thumbnail size on a single PDFsharp page:
http://www.pdfsharp.net/wiki/MixMigraDocAndPdfSharp-sample.ashx
You would call AddPage/RenderPage to draw each page in full size.
Another way that uses MigraDoc only: add a TextFrame() to the page header and set the FillFormat of that TextFrame to your background color. Set the TextFrame to fill the whole page.
This should work and it requires only MigraDoc (no PDFsharp code required).
I think I'd use the first method.