For starters, there's only user information in a system mdw if you're using access group/user security. (It's always on, but unless you set up groups and users and strip permissions from the Admin user you're not using it.)
Second, if you are using group/user security, you really should not be using the default workgruop file name system.mdw. It's installed on every machine that has Access. You will have a very difficult time telling which one is yours.
But enough of that...To answer your question. There's certainly no straightforward way to remove user info from the mdw. Someone somewhere may have a hack they've published to allow you to manipulate such things directly in the mdw. I haven't seen such a thing, but I haven't looked very hard.
Absent something like that, you'd have to somehow get an instance of your database and use object methods available from that object to manipulate the groups and users.
It's at least theoretically possible that you might be able to do such a thing from vbscript. If I were going to try that I'd write the code I needed within access first, to make sure I did in an environment that helped me out some. Then I start moving the code to my vbscript file.
Here's some vbscript that get an Access object:
dim o
set o=createobject ("Access.Application")
o.automationsecurity=1 'set macro security LOW.
o.opencurrentdatabase "\\spacehab.com\files\SHApps\EPRD\Live\eprd.4.51b.mde"
o.usercontrol=true
set o=nothing
What I've never tried is to run anything inside Access from vbscript like this. If you don't get a better answer or a better idea, I'll try it out one day soon and see what happens.