No one is advocating for "silent" installs; even in the wide-open-freedom days of early Windows, you still had to download and run a binary to install anything (browser exploits and such notwithstanding.)
You sandbox the browser
you put the installer on a different user
you make the installer always open a popup
you ask for the password/pin
If a JS script can bypass all of this then you have a bigger problem, the malware developers can easily already have a dummpy app already in the app-store that is signed by Apple, the installer signature is the last thing you should worry about in this case (better disable JS now)
Nobody is arguing that Apple's approach isn't more secure; they are arguing that the tradeoff (an additional layer of security vs. the right to install the software of your choice in a computing device you paid for) is not worth.
There are countless examples of this. Requiring everyone to strip completely naked to get on an airplane would absolutely act as an additional hurdle for a person with nefarious intent, but we don't do that because we acknowledge that there must be a fundamental tradeoff between our safety and our freedoms.