I don't know Ember.js but for the time being it should be the least jQuery hostile framework as Ember's code base seems to occasionally use jQuery itself (
https://github.com/emberjs/ember.js/search?utf8=%E2%9C%93&q=jQuery,
which isn't that surprising). That being said there seems to be some suggestion that jQuery shouldn't necessarily be the first tool to reach for when you are using Ember:
jQuery to Ember: How to Make the Jump Without Falling - YouTube and
No, really, Let Ember handle things!
The Top Mistakes Developers Make Using Ember & Rails - 4 Ember isn't jQuery, either
Basically jQuery is safe as long as nothing else is competing for access of the DOM - things change once a framework wants (preferably) exclusive control of the DOM. In general once you are using a framework
you should always find out whether there is a way to do something through that framework first before you get another library involved (even if you already know how to do it with that other library) or even use the browser API. Unfortunately every framework/library "has its own way of doing things" so there is always yet another learning curve to deal with (discovering what your tools are doing for you under the hood can sometimes help flatten the curve the next time around).
In the end the question that really needs to be asked much more often: "Is implementing this web application as a Single Page Application the best solution?"
For the time being counter-movements like
ROCA (Resource-Oriented Client Architecture) are being largely ignored (where jQuery libraries
are listed among others under
ROCA JavaScript Libraries). But there are cases where organizations have gone from front-end page generation back to rendering pages on the server side:
Improving performance on twitter.com | Twitter Blogs
Delicious Changes | The Official Delicious Blog
... so in some instances the issue should be more about avoiding SPAs - though be prepared for accusations of being "anti-progressive" and "stuck in the past".
Why I hate your Single Page App — Medium