First, the atemi issue: I think what you are questioning about the strike is not if it is weak, but dangerous (to nage). The strike that you are used to using is designed to transmit a great deal of force safely along well aligned realtively large bones in nage's fist and arm, lessening the chance of breaking something. In medicine we laughingly refer to a fracture of the 5th metacarpal (bone in hand leading to the little finger) as a 'Boxer's Fracture' knowing full well a real boxer would make contact instead with the kuckles of the index and middle fingers to protect their hand, and a 5th MC fracture is an indication of a drunk hitting a wall or locker.
The other side of the coin is, the smaller the contact size of the object, if mass and acceleration remain the same, the more concentrated the force transmitted---hence why we try to spread ourselves out in a breakfall rather than land say elbow or ankle first. So hitting with one knukle forward of the others, while putting that knuckle at risk, both allows for pinpointing a particular spot (nerve, weak bone, etc) on uke's body, and delivering a good sized blow to it.
I'm certainly no expert in atemi
so I'm guessing, but I think you'd use different blows for different reasons, and probably use the second type with a quicker/shorter distance, lighter amount of force than the first.
As for supporting your old dojo: you need to be where you are comfortable. Even well known, well established forms of Aikido, if they are not for you, they are not for you. I think body size, personality, and personal philosophy all play a role in what a teacher teaches, and what a student needs. Not every one meshes. Check out other places and go where you feel most comfortable and can learn. In the long run, attending classes where you, as a more senior student, canot accept what the teaher teaches will only cause more rather than less problems for the dojo, esp. among the junior students.
Attend several classes in you old dojo to be sure it was just not a phase the sensei was going through (even they have bad days, or try new things out for a while), but check out all of the other places, even the one you didn't think you'd like. After all, if your old dojo can change, perhaps it did, too. And yes, if you change dojos then for that year you will have paid two joining fees, but after that just one. That, plus a few mat fees while you are checking out the places, are worth it to find a place you like.