I don't believe there is a way to remove the header/footer region from certain pages of the report. The only options SSRS gives is Print on First Page/ Print on Last Page options in the Header properties, so you can only control the first or last page of the report with those options.
You can hide the elements inside of the header/footer regions through their visibility property. For example, you could hide the header/footer contents on pages 2 & 3 by setting the visibility function to the following for the items inside the header/footer regions:
=Switch(Globals!PageNumber < 2,false,Globals!PageNumber < 4, true, Globals!PageNumber >=4, false)
By hiding the contents in those regions, excel will have a very narrow empty row at the top of the page, but at least it won't create the funky merged cells.
If you want to completely eliminate headers when exporting to excel, you can do so by following the instructions in this article I wrote:
http://jaysonseaverbi.blogspot.com/2013/11/ssrs-exporting-options-for-excel.html