Why was it so important for M that Eve take a risky shot that ended up killing Bond, until he turned out to be faking it? Was the bad guy such an immediate threat that it was worth losing Bond?
It's not so much that the bad guy was dangerous. It's more that the hard disk he's stealing contains the names of hundreds of secret agents in active undercover operations. It's sacrificing one life to save hundreds.
Because movie lines are more and more picked from a grab-bag of the same phrases, and unfortunately, "Take the shot" is one of them.
The info was meant to be very important, and the value of all the agents' lives was worth more than that of one aging agent. Of course by the end of the movie we all know that there's no school like the old school, but according to the way of thinking at the start of the film the right thing to do was to sacrifice the old chap!