I think you are on the right track as far as first being concerned with easing them into fully resistance while minimizing injuries. To be honest the first thing you have to do is assess their physical conditioning to deal with this type of training. Alot of folks simply are not in shape enough to train this way without serious risk of injury, so I think whatever program you develop/implement it needs to take this into consideration. I think this is one of the best ways to reduce not only risk of injury, but to increase student's ability to deal with "combative stress".
Second thing, you can kinda do concurrently while getting them in shape, is to practice "positions of failure" (point of failure), that they will find themselves in during fights. that is, positions in which they cannot create distance necessary to fight. Once they learn the basics of the positions, they will find that a great deal of fear is reduced simply because they are able to recoginize the positions and begin to create the conditions necessary for them to escape from them.
What I like about these positions is that they can be practiced slowly, methodically, and safely, while teaching them how to deal with the realities of fighting.
I believe in literally working from the "ground up". That is, starting with the mount, rear mount, side control, guard etc....then working them to standing clinch work, both free (in the open) and against the wall/objects.
Again, these things can be done slowly, along with other drills/kata with folks and are great conditioning exercises to help them develop the kinesthetic awareness and feel while they are also getting in shape and learning to relax.
From there, you can then begin to create more distance and separation in the situation to more familiar drills/kata/exercises that we are used to seeing in Aikido.
I have found this to be about the best way in a dojo environment to condition folks for physical confrontation and to deal with the ensuing stress that comes from having someone else impose their will on you.
My criticism of aikido is that we start from the "outside/in". that is, we throw way too much of what I personally consider to be advanced material and expect students to "learn/keep up".
Once they are forced to deal with a non-compliant opponent hell bent on imposing their will and taking way that space from them, they tend to freak out if they have never dealt with having that space/position taken away from them.
Once you have spent a fair amount of time building the physical conditioning, kinesthetic awareness, and drills that they have committed to muscle memory...you can then begin to add the stress of aliveness on them in order to "pressure test".
Of course, there are various philosophies and concerns that arise from this type of training to include the whole "creates bad habits" argument when you look at it from a budo perspective...some of which I agree with from my own experiences and "bad habits'.
However, I think it all depends on what you consider your path to be and what your priorities are in training.
Yes, Toby Threadgill, has written some very good material on this too! I recommend reading it as someone has already suggested.
My advice if you are concerned with this type of training is to find a decent BJJ school, make friends with them and either cross train, or invite them to your dojo to train.
As of course, everything I have mentioned above, is the basis of BJJ and is why I think BJJ is a great art to complement your aikido practice as the range of combat and skills you will practice are almost the opposite approach in methodology from aikido so to speak.
However, there are only so many hours in the day and this does take time to train and cannot be trained in a weekend seminar...it would require a concerted effort over time if you really want to train this way.