This looks like a useful feature to add. It could be integrated into your PDF viewer (one page at a time), activated by a menu item or button.
The script that splits the 2-column PDF:
http://www.cs.toronto.edu/~hector/1colpdf
A sample PDF. Original:
http://www.cs.toronto.edu/~hector/jcan.pdf
Converted:
http://www.cs.toronto.edu/~hector/1col-jcan.pdf
Much better than the "zoom box" in the webkit browser, IMHO.