This is a really long-standing battle between user accessibility and user freedom. Any time a software system or platform or OS allows for people to do whatever they want without restriction, you end up with thousands of compromised systems out there. The alternative, in the past, has been to lock everything down unless users go into some kind of "Advanced" mode or "Developer" mode but then users just get tricked into turning that mode on anyways or more advanced users hand wave those restrictions away for less savvy users without explaining any of the implications.
This is the same pattern that happened with IE where users would install all kinds of toolbars accidentally and then get tons of data stolen or when the first iPhone was jailbroken and everyone wanted all the cool jailbreak features. People would jailbreak the phones of their parents, siblings, relatives, friends, etc. without really every explaining what was happening and what the potential pitfalls of that are.
Now, unfortunately, we're at the same impasse with browser extensions. They're super convenient for most people and are widely used but there's another vector of attack for people that aren't as savvy and don't understand the consequences. Especially when it comes to browsing history, payment data, and passwords, it's so easy to compromise a system now when you can hide it in something like a browser extensions.
The real answer is to do a better job educating people about what everything is but no one wants to do that. More skilled users just want to bitch about what gets taken away from them personally without acknowledging the giant elephant that is ignorance. There is so much advanced technology out there now that people don't even understand the consequences of the most mundane actions.
In my opinion, Apple's trying to do something about that even if it comes at the expense of a few power users losing some conveniences. If their past history is any indicator, they will bring back or improve up on this functionality so that power users get it back somehow but, in the meantime, the bigger and more pressing issue is what takes precedence.