The sentence ends with ἁγίου, placing more emphasis on an important word, instead of ending with ἐστιν, an unimportant word. Nothing more than that. As an inflected language, Greek lends itself to hyperbata like this, and they’re pretty common – nothing unusual.
Cambridge Grammar of Classical Greek, p. 710: “Greek constituent order . . . is not primarily a syntactic phenomenon. Instead, the ordering of constituents depends on their information status: a constituent’s position in the clause is determined largely by how new an important the information which it adds to the context is (in English, information status is mostly expressed by intonation).”
The sentence builds up to the important point, which is ἁγίου. The ordering ἐκ πνεύματός ἐστιν ἁγίου is only surprising in that it’s different from what an English-speaker would expect.
Joel (as I understand him) is right, I think, to question whether translating anarthrous ἐκ πνεύματός . . . ἁγίου as “from the Holy Spirit” amounts to “simply importing the later Church’s understanding of The Holy Spirit, and making it Matthew’s understanding by assumption.” The literal meaning of πνεῦμα is “breath” or "breathing, and one out of a range of meanings listed in LSJ (including “flatulence”) is “breath of life.” Perhaps τὸ γὰρ ἐν αὐτῇ γεννηθὲν ἐκ πνεύματός ἐστιν ἁγίου means simply something like “what was engendered in her is from a holy breath/source of life” (using italics to capture the emphasis place on ἁγίου by its placement at the end of the sentence.
In fact, the emphatic placement of ἁγίου seems to me, reading the Greek uninformed by theology, to show that the noun phrase ἐκ πνεύματός . . . ἁγίου – without article – doesn’t refer to a specific entity, “the Holy Spirit,” but rather that the sentence merely informs that the source of the pregnancy is holy, building up as it does to the important word ἁγίου.
I part ways with Joel in not characterizing ἁγίου as a predicate adjective. The predicate is ἐκ πνεύματός . . . ἁγίου. ἁγίου itself is simply an attributive adjective within the noun phrase.
http://www.perseus.tufts.edu/hopper/text?doc=Perseus%3Atext%3A1999.04.0057%3Aentry%3Dpneu%3Dma
But I’m not a Christian or even a believer of any sort, so take my comment for what it’s worth.