Not sure how you accomplished the page rotation in the layout, but the easiest way to deal with this is to set up as either portait or landscape, then rotate the spread view (in the Pages panel menu) for one page or the other. That leaves the actual page orientation unchanged for printing, but lets you see it rotated for easy layout.
If you actually have one real portrait page and one real landscape page, I'd export to PDF and print from Acrobat with the Auto-Rotate and Center box checked.