I'm bumping this old thread, because I'm a bit unsure myself of how this would work.
I did a Google Code Search for "server.cfg", and I found a lot of Half Life code. So I tried "default.cfg" and still didn't get much (changelogs and whatnot).
consider this: JAMP is compiled as a DLL and so..... you can basically do anything. You can use standard Win32 code to open/write/read/close any file you want.
As for logging in, you'd just add new commands in the ClientCommand in g_cmds.c (for example, "amlogin", "amkick", etc.)
awesome that someone is hosting the entire JKA source online, isn't it? o_O)
Now, to keep track of admins I think every player has a unique ID somewhere in their gentity. Or maybe you could track them by entity number. I really haven't messed much with player entities, so you're on your own there.
You also want to check to make sure that non-admins can't use /god and /noclip.
If I ever get around to making an admin system (sorta iffy), I'll post my findings here. =/