It's a usability trade-off. Defaulting to allow scripts to erase all your scrollback would be pretty annoying in a lot of cases. Ideally there would be a checkbox for this behavior, but Apple doesn't like config options.
One thing I wish terminals had was a "scroll up to the last place I typed something." I think that would solve your problem as well.
They are my scripts and I don't need "protection" from myself. Users don't use the command line so it isn't particular relevant to them - this is relevant to developers.
I fully agree it shouldn't be an option, and that generally being highly configurable is a way of abdicating responsibility for making the right choices in the first place, and ensures that not everything is tested (there will be too many combinations of settings).
In this particular case I just think Apple chose the wrong behaviour.
It's a usability trade-off. Defaulting to allow scripts to erase all your scrollback would be pretty annoying in a lot of cases. Ideally there would be a checkbox for this behavior, but Apple doesn't like config options.
One thing I wish terminals had was a "scroll up to the last place I typed something." I think that would solve your problem as well.