"Kill them both!" makes no sense
Dr. Evil screams this line at one point, when Austin timetravels, so he can save the female.
However, they don't have to kill BOTH of them. Think about it; EITHER one will do, and both will be dead.
If they kill the 'past Austin', then future Austin HAS no future, and of course continues being dead.
If they kill the 'future Austin', then past Austin only has long enough a future to last until the 'future Austin' dies, which isn't very long.
Either way, killing one of them kills both of them, as they are the same individual.
I kinda hate when movies treat time machines as some kind of duplicators; it doesn't work that way. The past Austin would very soon disappear into the time machine, and they wouldn't have much time to hang about, OR there would be a time paradox that would probably destroy them both.
In this kind of 'duplication' process, time is not only very limited it's also STRICT - one second too late and your timeline gets re-written, at least when it comes to the events following the time travel (and even before, because not entering the time machine alters the 'already-happened time travel').
In any case, just kill ONE of them and both of them will die. Dr. Evil's scream makes NO SENSE!