Since the standard narrative tense is the simple past, Kipling’s sentence
…and I believe that Lisbeth was always at heart an infidel.”
is not particularly marked within the time sequence of the story, but expresses an opinion of the chaplain’s wife, i.e., a general state from her point of view.
If the author had simply repeated was in the following narration, a reader might assume that Kipling was offering another general statement about the main character — at least until the time expression “at the mature age of five weeks” at the end of the clause.
The past perfect cues the reader to expect to hear about some event further in the past, in this case most likely Lisbeth’s baptism. It also aids in the switch in point of view from the chaplain’s wife to omniscient author. Thus it saves the reader the task of reparsing the sentence to place the event in Lisbeth’s earliest childhood once the time expression is reached.
Using the simple past instead of the past perfect is common when the difference in time to the prior event is not topical, which is not the case here.