Machine's aren't bad. They're especially good for size. If your doing 3 free-weight exercises in a workout for 1 muscle group then you can make it 2 free-weight exercises in the beginning and then 1 machine exercise. I think the hammer strength machines are good machines, and I also like them since they take 45lb plates.
But don't use machines for trying to develop absolute strength. Doing low reps on a machine or singles is just stupid. Stick to a 10-15 rep range with the machines. Use the fact that you don't fatigue as fast on machines to your advantage. Chest press machines are a nice alternative to high rep bench press since you can squeeze out the last few reps without worrying about whether or nor you'll be trapped under a barbell.
Except the leg curl. Apparently size wise it's best to train hamstrings around 8 reps when curling on a machine.
Beginners shouldn't train like lifters who are more advanced. Most people would do better BEGINNING by learning how to use free weights.
More advanced lifters shouldn't confine their thinking to believing that machines like Hammer Strength are a last resort. HS machines aren't like cable machines. They probably simulate free weight movement about as much as possible while including the safety someone lifting much heavier than average could use as a benefit.
That means relating HS machines to "rehabbing an injury" is to ignore how useful they can be to those who aren't "average beginners".
I don't see the use of machines as the sole province of advanced lifters. If you are advanced enough to where you are doing 9 sets for a muscle group in 1 workout, then you're advanced enough to use a machine or machines for the last sets of that muscle group in order to lift a moderately heavy weight for high reps without reaching fatigue as fast as you would with free weights.
But if you're training for strength, the only Hammer Strength machines you should be using are the Jammer Linebacker machine and the other iso-lateral machines that work a simultaneous push-pull motion.
The best powerlifters can max more in a free weight bench press than they can on a machine press.