I guess the platform installer doesn't support SQL 2000. Its not a mojoPortal bug, there is nothing I can do about it. The stack trace does not refer to any mojoPortal code, it looks like code internal to the deployment tool.
It doesn't really surprise me if they only support SQL 2005-2008.
All I do to package mojoPortal for MsDeploy is to make a few config files. It would be nice if they suported a switch to skip db creation, then you could at least use it to install the files and set permission and IIS config. If I learn of a way to configure it to do that I will certainly do it.
mojoPortal does still support SQL 2000 but I guess you will have to install it the old fashioned way.
Or, you could install the SQLite package and then replace the *Data.dll files with the ones from MS SQL version then set the connection string yourself in user.config.