McNamara wanted to shrink the Strategic Air Command and got ride of many obsolete / unuseful nuclear strike systems.
McNamara's idea of which systems were obsolete or otherwise not useful proved to be rather debatable, at best.
 
The B-47 may've been obsolete as a medium strategic nuclear bomber it however still had a lot of life left as reconnaissance and ECM aircraft.
AFAIK they were rapidly approaching the point where if the USAF didn't retire them, they'd retire themselves into smoking craters, regardless of any merits of the airframe.

Although as ELINT platforms, the RC-135 clearly had more space, weight and power. As an IMINT platform, any B-47 derivative was totally unsurvivable. And as a strategic plaform - whether bomber, missile carrier, or ECM - it was fundamentally too dependent on forward basing or tanker support.

SAC wanted rid of the B-47 in roughly the timeframe it went, because it wasn't an appropriate aircraft for their needs any more. They also wanted to replace it with some combination of B-52s and B-58s. That that didn't happen is due to a combination of the emergence of ICBMs and the changing strategic environment. Which, yes, McNamara had his part in. But another Secretary of Defense would also have reduced the size of the bomber force (maybe more, maybe less) in favour of missiles.
 
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