I am still pondering or wondering aloud about the following aspects.
Deacon Steven D. Greydanus recently wrote a good and thoughtful second review of the film, as always. I wrote about the film on my blog, a month ago, but I don't claim that it is technically a “film review.” It's a theological and spiritual reflection on the issues that the film raises. I continue in that manner presently, further inspired by the good Deacon. Caution: this time, massive plot “spoilers” are part of my analysis, so if you haven't seen the movie, stop now.
I am still pondering or wondering aloud about the following aspects. In so doing, I place myself in pretty much a “middle position” between the trashing reviews and the positive ones: as so often is the case with me. I tend to see truths on both “sides” of a given issue.
1. I don't think Fr. Sebastião was consciously apostatizing at the climactic scene, after hearing the voice (?) of Jesus. He was under extreme duress, wanted to help others (not himself), and thought he heard the voice of Jesus. He had a good motivation, and it was mixed with the weakness and vulnerability of the moment: after who knows how long a period of intense brainwashing and psychological torture.
But it is not at all clear to me whether Jesus would say such a thing in the first place. That is the key question about this scene, in my opinion. I personally don't think He would, but I am not “dogmatic” on the point.
2. Whether he apostatized later is the question. Deacon Steven noted: “Every year he must renew his apostasy, taking written oaths along with the fumie ritual.” This is a new element I haven't seen mentioned before. It's a yearly written assertion denying the Catholic faith. I don't see how it can be defended as somehow “not apostasy.”
At some point we have to take a firm stand that there are lines beyond which no Christian can go, even under pain of torture and death. We can be compassionate about threatened torture and traumatic emotional distress all day long (I was, repeatedly, in my first piece), but the lines still remain.
My own theory is that the apostasy (incomplete or complete) of both priests was largely due to difficulties in understanding why a nation like Japan could so thoroughly reject the gospel, and trying to make sense of other religions: their purpose, and how much may be true in them: very deep and difficult questions involving “salvation outside the Church.”
3. Deacon Steven also wrote: “Rodrigues serves the magistrate by examining imported artifacts for Christian contraband.” Yes, he does. And in so doing, Christians may very well have been killed as a result, having been exposed by these acts. This is also indefensible.
4. Fr. Sebastião gets married, thus breaking his sacred vow. That is no trifling matter at all: the gravity of which needs no further explanation to a Catholic readership.
5. Countering the “negative evidence” of #2-4 above is a seemingly reluctant absolution given, and his wife secretly putting a crucifix in his hand before burial. Thus we have (slight) “ambiguity.” But we would expect that. I don't see that these two “anomalies” overcome the manifest evidence of his public apostasy.
Thus, I think we can very plausibly conclude that he apostatized (just like the Liam Neeson character), while retaining a few elements of his Catholicism and priesthood. It was a new “synthesis” at best: no longer bold and consistent as before, but outwardly Buddhist, and Christian only inwardly and secretly (that is, merely private, subjective religion).
Is the film trying to “endorse” a syncretistic notion of Christianity + Buddhism? Some of the later dialogue possibly suggests just that. This is the danger in an “ersatz ecumenism” which isn't for the purpose of rejoicing in actual common ground and seeking to bring folks to Catholicism (authentic and orthodox Vatican II ecumenism); rather, it presupposes indifferentism and the essential equality (or relativity) of all religions from the get-go.
The film chronicles the downward spiral of apostasy, though – maddeningly –, in not enough detail after the climactic scene. We can understand it on a human level, but it's not enough to excuse his latter actions. We ought to sympathize regarding difficult, existentially agonizing experiences, but rationalizing or justifying sin (apostasy) is not good. The following stirring, strengthening words from Jesus come to mind:
Luke 21:12-15 (RSV) . . . they will lay their hands on you and persecute you, delivering you up to the synagogues and prisons, and you will be brought before kings and governors for my name's sake.  This will be a time for you to bear testimony.  Settle it therefore in your minds, not to meditate beforehand how to answer;  for I will give you a mouth and wisdom, which none of your adversaries will be able to withstand or contradict.
Writing a yearly statement of continued denunciation of the Catholic faith, committing acts that will help get Christians captured and killed, and breaking a priestly vow to get married is quite inconsistent with the above.
Fr. Sebastião Rodrigues is a broken, fundamentally compromised man at the end, and his public apostasy would be seen by the Catholic populace at large as scandalous and disheartening: precisely as was the case with the Neeson character.
That said, I reiterate my contention that the film doesn't “glorify” apostasy. It simply portrays it as it is, or often is. It's dedicated to the Japanese martyrs, after all. Not every account is an advocacy of some point of view.
Apologists like myself write about and explain “sinners in the Church” as a thing we should expect (casually predicted in the Bible): so we shouldn't be shocked to actually find sinners, or to see them portrayed in a movie. Since this film also movingly, favorably dramatized examples of faithful Catholic martyrs, I think it can be considered “fair” in its cinematic portrayal.