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I was reading the book The Unwritten Rules of PhD Research by Marian Petre when I came across the following idiom:

... anyone with an armchair and reasonable general knowledge can usually find several reasons for querying the representativeness of a sample without much effort. These scruples tend to be slaughtered on the altar of expediency the moment that the questionnaires go into the post (questionnaires are a favourite method for collecting large and dubious data sets)...

A google search shows this is not an extremely common phrase. What does it mean?

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This is a metaphor. The key words are:

AHD altar

  1. An elevated place or structure before which religious ceremonies may be enacted or upon which sacrifices may be offered.

For slaughter, see sacrifice:
AHD sacrifice

a. The act of offering something to a deity in propitiation or homage, especially the ritual slaughter of an animal or a person.

Macmillan expediency

the use of methods that produce an immediate result or solution to a problem, but may not be fair or honest

So, scruples are allowed to die just to produce some immediate result.
In the context of the quote, it means carefulness or reservations about the soundness of survey data are ignored to get to the desired result, the publication of PHD research.

You may find more results searching for the metaphor with the wording "sacrificed on the altar of", with the last word being left blank.

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