Actually, I frequently archive production modules of that size. Maybe my network's just better tuned, but I can live with the time it takes.
However, I exclude files of any size from Version Control unless there's a reasonable expectation I'm going to retrieve them. Work files and directories are on the projects ignore list.
It sounds like what you want is a client smart enough to difference binaries BEFORE they're sent to the server, and I don't know of any. If you're talking JAR/WAR/EAR files or compiled code, there's an extra challenge. Today's optimizing compilers are smart enough to make significant global changes to the resulting code based on fairly minor alterations to source code. Including moving whole blocks of code in and out of line, hoisting loop code and much more. In simpler times, you could use a tool like IBM's ZAP utility and modify a few bytes and the difference file would be miniscule. No longer. Not unless you're coding in assembler or have one really dumb compiler like those in common use back when zapping was standard procedure.
I can think of 2 things that might alleviate your issues, assuming that you can't simple add the offending files to cvsignore or its equivalent:
1. Limit people to nightly checkins. Personally I'm not good at that, but allegedly some teams are.
2. Teach people to do partial checkins. This is a bit risky, since it's easy to do an incomplete checkin when a complete one is needed and vice versa. A variation on this is to target your builds so that the build results go into a separate directory and that directory is only checked in at end-of-day.
I actually did something like option #2 at a previous employer. All production modules had to be placed in CVS for the operations staff to retrieve. For their convenience (and ours) we had a special project that held the deployables. In order to avoid having everything in one large directory, we made subdirectories for the various products based on their toplevel package qualfiers (for
Java projects) or their equivalents (for non-Java projects).