Yes, a cathedral can be referred to as a 寺. Here's Nogami Toyoichiro doing just that. Forgive choppy translation, please:
ノートル・ダームの大寺はローマ時代にはユピテルの神殿のあった位置で、イル・ド・ラ・シテが「パリの目」なら、ノートル・ダームはその「瞳」だといってもよい。ここに寺の建てられたのは四世紀の半ば過ぎで、初めは聖エティエンヌと呼ばれていた。それを聖母（ノートル・ダーム）に捧げる寺にしたのはいつ頃からかよくわからないが、ヴィクトル・ユーゴーに拠れば、シャールマーニュ帝が最初の礎石を置いたというから、そうすると八世紀の末か九世紀の初めであっただろう。
The 大寺 of Notre Dame is located where the ancient Roman 神殿 to Jupiter was, and if the Île de la Cité is the "Eye of Paris", we can surely call Notre Dame the "Pupil". It was the latter half of the fourth century when the first 寺 was built here, which initially was called Saint-Etienne. It is not clear when that was made into a 寺 to the Holy Mother ("Notre Dame"), but, according to Victor Hugo, Charlemagne laid the first foundation stone, and so it must have been in the late eighth or early ninth century.
Nogami's chronology doesn't match up with the Wikipedia explanation, but as you can see there is clearly precedent for using this sort of terminology for Christian churches and even Notre Dame itself. I've seen 本山 used for people-of-the-book religious buildings, and I've seen 教会 used to refer to "the Church" (the organization) and 寺 for "church" (the building). And let's not forget terms like 南蛮寺 ("Barbarian temple") from the early Christian era in Japan...
However, as dainichi says, in contemporary Japan (Nogami's piece apparently dates from 1941) we would generally expect "church" to be translated 教会. This is I think a reasonable observation. The reason for this is that Japanese culture is becoming more familiarity with Christianity and other "world religions," which means two interrelated things: (1) increasing awareness of the distinction between them and Buddhism (i.e. they aren't just "corrupt sects" of the same everything-except-Shinto "religion", they are a different religion); (2) increasing specialization of and familiarity with vocabulary, so that even non-Christians know that Christians call their place of worship a 教会 and believe it distinct from a 寺 (which is also "sharpening" as a concept because of cultural self-consciousness).
So, why use 寺 in this translation if it is "possible but marked"? This is something I cannot answer, although someone else might be able to. I can think of several possible explanations, though, one or more of which might be true:
- Timing. /tera/ is two morae shorter than /kyo:kai/. This might have been important.
- Mood. In this story in particular, Notre Dame is not a modern, well-lit place of worship, but rather an ancient and foreboding place of worship. The translators may have felt that the implications of 教会 were too tied in with modernity and so on, while 寺 feels more "old"
- Characterization. This is sort of tied in with "mood", but perhaps the translators wanted to make the characters and situation seem more old-fashioned and picturesque. Here too using 寺 could help.
