SF is still a harder offense to defend. Much better running game, their system and WR separation are phenomenal and when Williams is healthy they are pretty elite at protection. The offense is stacked and designed so that you cannot make good choices against them. They're built to destroy zones and if you decide to go man to man, if your pass rush does not get home they WILL get you on the crossers and YAC plays.
The Cowboys offense is excellent, but lack of run game and questionable line play at times is going to be a problem.