One way to do it is to lock the arms etc, before you apply the walk cycle. Locked actors don't get affected when you apply a pose, or use the Walk Designer. After applying the walk cycle, you can unlock the actors.

Alternatively, fix it after the fact. Say the walk starts at frame 20, and the arms etc are in the correct position at frame 19, make a key frame at  frame 19, apply the walk cycle, then delete frame 20 and above from the arms.