There is also a (strong) possibility that Pages is making a creeping error in calculating line spacing and positioning, which is why this problem occurs deep into a very long document.
As Yellowbox suggests splitting any long document is always a good idea. Both Indesign and Quark Xpress do it as a matter of course, combining the results into "Books" which are the sum of those separate documents.
I don't have a document that long handy, and I haven't seen this myself, but it occurred to me that Numbers has somewhat similar problems when the zoom is set to something other than 100%.
I wonder if you set the zoom to 100% when the window is displaying the beginning of the document, would it still have this problem when you move to the end? And, if it doesnt, could you then change the zoom to a readable setting without losing access to the whole page?