It's a pretty small change to the makefile.
I posted a sample working makefile in arduino issue #650:http://code.google.com/p/arduino/issues/detail?id=650
I hear you on the backward compatibility issue. Off the top of my head, I'm not
quite sure what would trip up with the new stuff as I think it essentially does the same
thing just in a single command.
However, you never know.
It is a bit ironic that the avrdude command doesn't properly support the Atmel AVR dragon....
and that the avrdude maintainers seem uninterested in fixing it, especially since it is less
than 6 lines of code to fix it.
If you have some pull on the IDE and they are concerned about making the change to single command,
can they at least up the delay between the two commands?
(They already have a delay, it just isn't long enough to allow the Dragon to work with the existing avrdude command)
But since they already ship a version of avrdude with the IDE, would they be interested in shipping a fixed avrdude?
I have patches for that fix as well - see issue #650.
If avrdude is fixed, then you don't have to modify the IDE or the Makefiles.