Alas, there isn't much that we can do about it at the moment. This is due to a limitation of PDF files colliding with a limitation of eInk displays. Different vendors deal with these limitations in different ways and clearly Kobo's implementation doesn't satisfy you. (It doesn't satisfy me either, which is why I have a Vox to deal with PDFs and a Touch for ePubs.) It is worth considering that no single solution will satisfy everyone since all of these solutions are kludges.

You have a couple of options here. You can try making a constructive suggestion to Kobo to improve page turning when zoomed in (easy to implement, thus realistic) or to add an option to reflow text in PDF files (more difficult, thus less realistic). Since they issue frequent updates that improve their products, they may be willing to listen. The second option is to return the Touch and find a reader that is more geared towards your needs.