You mean software engineering or computer science?
With computer engineering, you're supposed to learn something about hardware as well. Teaching Java-only for computer engineering would be, well, stupid. I don't think you
could teach Java very well for that, as I don't know of any embedded circuits that come natively with a Java VM. (Would that even be a VM anymore?

)
By all rights, something in CE should be taught using a lower-level language, at least C.
With Software Engineering, I could at least see you specializing in something like physics or art or some kind of business/education software and never really needing to know about memory management, because the computers/applications you'd be using would mostly be mathematical or UI-based in nature. You'd be shooting yourself in the foot if you learned only Java and ever wanted to do anything else, but I think you could successfully lead a programming career with just Java.
I can just see it now...
"So I built this media player. It's awesome! It's got an LCD twice the size of an iPod, has an 80G solid state drive, but it only costs half as much to make with my connections as it costs to buy an iPod."
"Sweet, play something on it."
"Err...I can't."
"What? Why not? You've been working on it for 6 months, isn't it done?"
"Yeah, I'm sure it is. It powers on and everything."
"So what's wrong?"
"Well, I can't actually do anything with it. You need to know how to at least compile a C program to do anything with it."
"Oh, that sucks. Well, I guess we can always wait 'til Apple invents it, and then reverse-engineer their software."
"Sweet! That's a great idea!"