This is easy since pdftk 1.44 which added the shuffle operation allowing different transformations on odd and even pages (amongst other uses).
If you have an older version of pdftk, you can use this Python script with the PyPdf library. (Warning, typed directly into the browser.)
#!/usr/bin/env python
import sys
from pyPdf import PdfFileWriter, PdfFileReader
input = PdfFileReader(sys.stdin)
output = PdfFileWriter()
for i in range(0,input.getNumPages()):
output.addPage(input.getPage(i).rotateClockwise(90 if i%2==0 else -90))
output.write(sys.stdout)