A couple of thoughts...
1. Could the rule change actually benefit the HUNH?
The whole purpose of the rule change is to give the defense ten seconds to substitute. That's not a lot of time if you know what goes on with defensive substitutions. They 99% of the time are not giving two shits about their players sucking wind. In fact, most teams keep the same secondary and linebackers on the field the whole game and rarely give those guys breathers. Defensive linemen get changed out more often, but even then, it's usually a big change out by series.
Defensive substitutions happen to match personnel and field situations. 3rd and long? Send in a nickel for a linebacker. 3rd and medium? Send in the quick pass rusher and the nickel for the fat guy and linebacker. They brought in a fullback and a tight end? Let's substitute our fat guys to match their heavy set.
What the ten second rule does is allow the defenses to rush their guys out onto the field and slow down the pace of the drive. Yes, this helps them.
But on defense, you have to read and react. The main reason why a HUNH hurts a defense - especially one like Saban's - is that it's moving too fast to line up correctly, audible the coverage or blitz, get into proper position on the defensive line, get your eyes and head focused presnap, read and react after the snap while running the play.
So they get ten seconds from the time the ball carrier is whistled down.
The offense hurries to the line to get lined up. The defense in ten seconds will have to sprint a new set of legs onto the field and the old, fatigued set of legs off the field. By the time they get into the defensive formation, are they aware of what the offense is doing? Do they have more time or less to get lined up and read and react to the offense? Who would really be better at stopping Malzahn's "Let's run the same successful play as many times in a row until they stop it"? The defensive guys that just faced it or the ones who are sprinting 25 yards onto the field for the first time that drive?
2. The ball carriers will delay the game and the refs will have to be petulant and ridiculous to call a penalty on them.
Artis-Payne hits a six yard run and is tackled near the sideline. According to the rule change, if I'm reading it correctly, that's when the ten second window begins. So Payne holds onto the ball for a second or two while getting himself up. He looks around. "Which ref gets this? Oh you? Wait was it you? Oops sorry I didn't get a good toss to you." The ball bounces around while the ref picks it up. The ref tosses it to the ref that spots the ball. The ten seconds are nearly up, and Auburn's offense is standing all over the field. Gus gives the signal. "Run it! Run it!" Boom. Offense lines up in a new position as soon as the ten seconds are up, hikes it, and the defense still didn't have time to read and react.
3. The bullshit of the "protecting fatigued players" aspect. Sure, Alabama will have fifteen 5 star defensive linemen they can run out there every play, but not every team is Alabama. Most teams only have a two deep to rotate into the game on defense. Even then, their two deep isn't the best option to stop a good offense.
So if they want to keep their players fresh and "uninjured," they'll have to run them onto the field often. In order to get them out there on time with the ability to read and react, they'll be forcing them to sprint 15 yards on and off the field over and over again all while telling them to hurry up, line up, read, react, fight off blockers, chase, tackle, pop up and get ready to do it again.
They will be just as tired running wind sprints as they would be defending their side of the field against a HUNH.