I guess people are unaware of the various malicious rootkits that have cropped up?
If you're serious about this stuff binary thinking is a mistake. It's not a question of whether rooting is possible or impossible. It's a question of under what circumstances it can be done, and under whose control.
Also, "conflict" is the wrong word here. It's a question of competing concerns not conflicting ones.
We probably want root access to be under the end-user's control, but in such a way that minimizes the ability of malicious parties to exploit it.
e.g., one way would be to allow anyone to easily install any root they want, but to disallow software from, say, the Apple app store from running on such "rooted" devices. While that gives end-users control and would mostly prevent malicious actors from getting things they want, it's probably not what most user's would want. They probably want to run all their regular software along side the root software.
Another way would be to allowing people to easily install software as root, and allow software from popular app stores to run on it. That gives users max control, but is pretty easy for malicious actors to exploit too. People aren't going to be too happy with this when some coupon clipping app starts emptying people's bank accounts.
These are just examples to give the idea of the range of possibilities. The real answer needs to be a lot more nuanced than this. The point is, pretending there aren't issues doesn't get us anywhere. You might as well have no opinion on this.