I didn't know that computer science majors use AutoCAD that often these days, but in any case, AutoCAD should run fine on 9400M--I didn't even have dedicated graphics when I started using AutoCAD 15 years ago, and I don't think the usage of AutoCAD has changed all that much throughout the years.
Of course, it is a completely different story if one works extensively with 3D drawing or video. But if that's the case it is probably wiser to spend the $750 difference between a 15" MBP with 9600M and a 13" MBP on a desktop with 2 screens. A 13" MBP and a desktop in conjunction would give more processing power, more screen estate and higher portability than a 15" MBP alone.
I was a CS major and we didn't really do much that required a beast of a graphics card. Just a lot of programming, and writing papers and researching for your gen ed's and a few CS courses. If you're doing graphically intensive stuff while programming anyway that's different though.
There are a lot of reasons a Mac is great for a CS student, such as ease of coding for it, integrated development tools, UNIX-based foundations (Yes, Leopard on Intel can actually be called UNIX, Apple paid lots of $$ for that), all the key open source software and libraries work great for it, and so forth.
And AutoCAD has changed significantly over the years, but is still Windows only so VMWare Fusion or Parallels or Bootcamp with Windows is necessary. The hardware required for AutoCAD just keeps going up and up, so you need a beast of a computer to use it without an upgrade for a while. But for CS AutoCAD is a non-issue really, but it depends what kind of engineering student you will be to see how much benefit you can derive from having it.
Oh, and you WILL want to get VMWare (I ordered it over parallels for my new MBP) and a Windows license and media (XP Pro, or Vista Business or Ultimate, or Win7 eventually once stuff supports it) because you will have that one random class with the software that will ONLY work on Windows that you need to use, or that one website that only supports IE, or whatever. Just the reality of today's environment... academic, business, government or whatever. Thank goodness we have Intel and great virtualization support for Mac's now!
Oh, and if you're CS or IT or Engineering, and you can use MSDNAA, USE IT. Free (or almost-free) Microsoft operating systems and development tools you will never again get freely once you graduate, works great virtualized on Mac too! Also, you can get awesome discounts on MS Office (check with your school's IT, techstore, or bookstore for special programs and options) and Autodesk, Adobe, and other stuff.