I imagine you could send 0x80 by holding the ALT key, and then typing 1 2 8 on the numeric pad. This is the classic keyboard control for getting special 8-bit character codes input.
The protocol is designed for automated interaction rather than user terminal input. It's not really a command line monitor, and not tolerant of mistypes, or backspaces.
I can understand not wanting the SAM-BA host side application, it has grown rather big and clumsy over the years. On the other hand, I'd probably be writing a simple Win32 console app that talked to the COM port directly.
Some of the SAM9 docs might provide a better review of the protocol, and the binary vs terminal modes.
Personally I found this reasonably helpful
http://sourceforge.net/apps/mediawiki/l ... ion:SAM-BA