You are right, msgplus.exe can already be used this way. However, it was never meant to be run standalone and needs some registry keys to function properly.
In Messenger Plus!, a special application called Log Viewer aill be included. You'll be able to use the application with its exe only, nothing else will be required (so you can keep a copy of it somewhere, like in your logs directory if you want to be sure you'll always have a way to decrypt your files). This program will also have some clear command line parameters to let you encrypt/decrypt file or change your password in a given file. Launching it without parameters will display a nice GUI that lets you browse your logs and see everything nicely in an IE control.
You'll see all of that in the beta Cookie
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