Sgt Barker is correct, stacking limit on pillboxes cannot be done other than the formation of house rules if that is what someone wants to do (but one of the missions of the _Alt scenarios is to eliminate all house rules).
As Sgt Barker also states, the practical (and easiest) solution is indeed with tweaking the fortification levels of the beach hexes. If it is deemed that some are too tough then BUNKER can be changed to Bunker, Pillbox to BUNKER, or PILLBOX to Pillbox. If anyone has any specific suggestions on which hex to downgrade then I am all ears *hint hint*. ;)
Some good recommended reading on how tough Omaha was and the basis of the current Omaha beach fortification levels:
http://www.army.mil/cmh/books/wwii/100-11/100-11.htm