So if I get this right the issue isn't so much if companions die or not but that you have to baby sit them trough everything?
If the companions had better AI and the player more sophisticated and easier controls, would it be acceptable? I mean we are after all in 2015 and not 1995. I surely would hope that SOME improvements can be made here - and some games did!
I think the best way to handle it would be to make it simply optional, if it is really to much of a work to make the comanions not suicidal. It definitely can't be much work to create a small check box in the menu. The game could tell the player at the start that if your companions die now they will be out permanently unless you activate it in the gameplay options or something like that.
I am just not a friend of immortal NPCs. I think in todays gaming you have many tools at your hand to get around it. There are enough old RPGs that allowed you to kill everyone, if you wished so. That's of course just me but Companions for me don't feel like companions if they just take a short nap after being hit by a rocket luncher and getting beaten by several monster/raiders/what ever. I agree that Fallout 3, Oblivion, Skyrim etc. are not very companion friendly games, there they are just pack mules with a voice and nothing more.
But it is more a question of how much attention you give a good companion system with the commands, the AI and all that. How much control you give the player. For example to give your companions armor, stimpacks and other equipment. More sophisticated command and behavior options could make it easier to navigate your companions trough combat. Telling them to retreat if they loose 50% or 70% of their health, running away, using a stimpack - if they have any, and to return to the combat. Or not to attack a target before the player started the first attack. Or only attacking targets that use melee weapons. And so on and so on.
It all depends how well it is done. I can of course only talk for my self. But I always care more for those companions where I know, if something bad happens, they will die. It makes it simply more plausible and believable. At least for me.
As frustrating as this can be, it would offer a perfect opportunity of choices and consequences. If you chose to be reckless with your companions or if you simply had bad luck ... well it's either reload, or continue with the consequences. It would at least allow you to have a sense of role playing and permanence to your play trough. In other words, things matter. With immortal companions you can always charge head on in every engagement, without ever to think about preparations or if you're ready to attack.
Like I said earlier, it could be completely optional and that way you would have the best of both worlds. It can't be a bad thing to give people choices here.
I am pretty confident that mods will change that anyway making all immortal NPCs mortal. However, that should not be any kind of excuse to have them in the first place, cauz moders will fix it!