When pasting text into the terminal, joe should not re-indent or re-wrap that text.
There is currently a similar feature in joe called "joexterm", but it requires xterm as terminal (I'm not aware of any other terminal supporting the required underlying feature of base64 paste), requires manually enabling the "joexterm" option which is harmful on other terminals, requires mouse support enabled, and then disables autoindent and wrapping if pasting text using the mouse.
There's a much more standard extension called "bracketed paste mode" supported by many terminals. It's safe to ask for this feature, causes no harm on terminals that don't support it. It has nothing to do with mouse support. If data is pasted by any means (no matter if it's mouse or hotkey), it's guarded by special marks so the application knows it's being pasted rather than typed in.
Please see my patch which adds support for this feature.