TL;DR: Susan is expressing pity for Miss Gilchrist.
The Wikipedia article on lady’s companions explains the social background to the situation in the novel (the article also contains spoilers for After the Funeral, however). Formerly, upper-class women (“ladies” as Susan Banks puts it in the novel) who had neither money nor a husband were faced with the choice between losing their class status by earning a wage, or taking roles that were considered respectable, such as acting as paid companions to upper-class women of means.
The role of companion was inherently ambiguous: neither friendship nor employment but combining elements of both. Servants took orders but could give notice and seek work elsewhere if exploited, but companions were more precariously placed. Susan implies that Miss Gilchrist had been made to do the work of a housekeeper or servant without having the freedom to leave.
In “get it taken out of them”, the sense of “take out” that we need is:
take out, v. 7. To take (something) from (a person) in compensation.
Oxford English Dictionary.
So Susan is saying that Cora got more than enough work out of Miss Gilchrist to compensate for the (no doubt inadequate) allowance the latter was paid.
Companions feature in several of Christie’s other novels and short stories:
|The Mysterious Affair at Styles
|The Mystery of the Blue Train
|Cards on the Table
|‘The Nemean Lion’
|A Murder is Announced
|They Do It with Mirrors
|‘The Under Dog’
The figure of the companion is useful for Christie because of the ambiguity in the relationship between companion and employer. The subservient position of the companion gives rise to resentment or concealment, since she cannot speak her mind for fear of alienating her employer. A couple of these novels feature the issue of whether the rich employer will compensate the poor companion in her will. I think this is what Susan’s referring to when she asks whether Miss Gilchrist and Cora were “on intimate terms”—that is, did Cora like Miss Gilchrist well enough to leave her a significant sum in her will?
The Second World War, in which millions of women entered the workforce, demolished much of the remaining class prejudice against earning a living, so that companions vanished more or less completely. Even in 1953 when After the Funeral was published the character of Miss Gilchrist was something of an anachronism.