Easier to pick up? Not really.
JS is only "easier to pick up" and use for "building websites" in a very limited sense. It's all a matter of what you're picking up.
Once upon a time, when web pages were mostly HTML, JS was mainly used for enhancements and tweaks, and scripts didn't contain much beyond procedural code and simple inheritance. The language specification scarcely changed for ten years. It sounds like the course is teaching this kind of antique JS.
These days, JS is a hotbed of crazes, functional programming enthusiasms and novel frameworks. There are at least three language versions in common use. Knowledge gained on version N of a framework will be useless when version N+1 is released. Web sites now consist of large single-page applications, and their syntax and code organisation will be utterly baffling to someone who's been taught "window.alert('Hello world')" scripting.
Regardless of opinions about the relative merits or potential longevity of the two languages, Java has more overall consistency between APIs and stability between versions. Students who have completed an introductory course in Java stand a better chance of finding their way around real-world applications than they do in JS.