Some dojos care more about Japanese traditions and some just not.
I don't believe that folding you sensei's hakama will make a difference in the way you practice Aikido.
In my experience, I have never seen my sensei asking someone to fold his hakama.
I would like to add the fact that my Sensei is not Japanese. Probably to a Japanese sensei that will be as important as teaching techniques.
I'll have to note that in over a decade of training in Japan, in a number of different dojo, I very rarely saw anybody fold a teacher's hakama. For the most part (99%+), they folded their own.