But it would've been really offensive to have it seem like Cap played a big part in the war on the Axis instead of the normal soldiers. Having him fight a group like HYDRA (who WERE all Nazis until they broke away) keeps the potential offensiveness down.
I don't think it offended anyone to see Indy fighting the Nazis. And it's not like these are specific WWII battles we're talking about. It still would have been Red Skull doing his crazy, James Bond Villain thing in his mountain hideout, but he would be guarded by actual, authentic-looking Nazi troops to add that extra dose of believability.
It definitely wasn't a big
issue for me, but I can see how it might have helped the movie a bit.