I found a reference about an undocumented method about changing a full instance collation coming from Paul Randal.
Info quoted from the blog of SpaghettiDBA:
"The method relies on a startup parameter that allows changing the
server collation when combined with a couple of trace flags:
sqlservr -m -T4022 -T3659 -q"new collation"
Trace flag 3659 allows logging all errors to sql server logs
Trace flag 4022 forces SQL Server to skip startup stored procedures
(if you have any).
Startup option “-m” forces single user mode.
Startup option “-q” rebuilds all databases and contained objects into
the specified collation, without reinstalling the instance."
Paul's document with undocumented params is: Undocumented tools and trace flags.
Not very sure it's working on SQL 2000, because I didn't see a clear reference about the server version, but it's worth a try.
I'm also not very sure that it's so hard to rebuild the master db, as in SQL 2000 there was a nice little tool that did that without any user intervention (Rebuildm.exe - found in ..\Program Files\Microsoft SQL Server\80\Tools\Binn directory.).
If you have already some databases to convert you might try the project SQL Server 2000 Collation Changer - it's useful for changing the collation for a database and all underlying objects.