In the "Angular Way," there is a strict separation of concerns. The Controllers aren't supposed to know anything about the DOM (Document Object Model); the Controllers simply manage the view-model and leave it up to the Directives to "glue" the view-model to the DOM. In the "Angular Way," the Directives are the only thing that should know about the DOM. And yet, you can inject the $element into your Controller constructor and you can pass the $event into your Controller using scope methods. Which begs the question: should injecting the $element and $event objects be considered an anti-pattern in AngularJS?
Personally, I lean towards Yes on this one - that it is an anti-pattern.
However, I will caveat that with saying that sometimes the simplicity of doing so (injecting $element or $event) may substantially outweigh the complexity of keeping things separate. I don't think there's anything that can't be accomplished with $watch() bindings and event-bindings inside a link() function. But, especially for one-off events, mutating the $element directly can be more straightforward than worrying about $watch() bindings.
A good example of that might be the native Form Controller that ships with AngularJS. In the Form Controller, the $element injectable is used to add various pristine, dirty, and other state-indicating classes onto the Form element in response to method invocation (ex, form.$setDirty()). Could each of these classes be added or removed by a $watch() binding in a link() function that was observing the changes in the Form Controller's view-model? Probably. But, it may be hard to argue that such a strict separation would make the code more peformant, easier to reason about, and easier to maintain.
So, personally, I think you should avoid injecting the $element object into the Controller constructor or passing the $event object into a Controller method. I think doing so blurs the lines and breaks-down the strict separation of concerns outlined in the "Angular Way." But, as Morpheus said about rules, "some of them can be bent; others can be broken." Just make sure you're operating based on educated decisions.