I hope this helps as I have a similar experience and I am no expert in throwing a tomoenage.
You would have to be a nut not to fear the throw. I think it was initially designed to have the uke land on his head. Well it if wasn't and you wanted to make the technique deadly, it isn't hard to do.
Let me assume the tori wasn't very skilled in the throw, thus the accident occurring. I am sure you are going to come across others who are just as unskilled. Therefore I recommend, because it helped me, not to assume that a person throwing me knows what they are doing. With that said when I practice ukemi I practice with that in mind. I never let my guard down.
I will assume the tori probably collapsed his arms during the throw. It is important that the head is tucked in enough to protect the head more. All too often I see people with their chin sticking out in the middle of being thrown. They are either looking at the tori's face or where they are looking at the place on the floor where they think they are going to land. Not good.
A ridged core/abs is without question, those abs really need to be contracted. Doing so helps with the rounding of the back, and allowing the head to tuck in tighter. Helping to proved the least amount of skull surface contact with the floor- when things go bad. Ideally you land across your should when thing go bad. Too often I see novices who arms lack the strength needed to support the body durring the throw. Rather the extention of the arms, like being half way through a push up. People who are experts at taking this fall don't put so much strength in the arms and they fool the novices into thinking the arms don't play a part in protecting you from the fall.
Something, I find important is when tomoenage is executed, as a protective measure (that is what ukemi is anyway), you push off the floor a bit as you start to go forward to get the height to clear the tori and roll away- when things go bad. Ideally, if things go bad and you don't clear the tori you have enough momentum in some circumstances to brake-fall or land on across the upper back shoulders below the base of the neck. This takes a bit of practice and timing to get right. It is like a dance lift very subtlely done. You don't want to launch yourself too much. Again something to practice. Take your time with it.
When practicing to take the tomoenage having extented arms, head tucked in good, rounded back/tighten core, and a bit of a push-off at the start will help in lessening injury. I would rather land on the back of my head when it is tucked in then on the crown of the head. And also do a lot of neck exercises to strengthen the neck muscles.
If tomoenage is exacuted correctly there is never a chance of injury. If everyone did perfect technique then there would be no reason for ukemi-considering the tori isn't out to kill you. But that is unrealistic.
To rap things up, I don't blame you for the reason the throw makes you uncomfortable. I am surprised, having a family, the leg numbness didn't have you stop martial arts. What I am suggesting is what I have done to avoid injury many times. It helped me. That is all I can say. Like I did, maybe find a good judo class that has a Judoka that is flawless in throwing i.e. tomoenage, and or they have real good ukemi and experience to help you fall safely when a throw is bad or goes bad. Personally, I can't think of any other art that pays so much attention to ukemi to the study and practice of ukemi and it's safety then a good judo dojo, I mean that is what the do, it is their niche.
Just sharing my experience, and hope it helps. Kudos to all.
