I subsequently discovered that the answer to my question is basically addressed in the Gemarra in Sotah 26a (and 32b, see below):
במתנוונה דרך אברים מהו דתימא הא זנויי זנאי והא דלא בדקוה מיא כי אורחיה משום דבאונס זנאי ולגבי כהן אסירא קא משמע לן
The Gemarra says that the Mishnah (on 24a) is discussing the case where a woman, after drinking the sotah waters, starts to deteriorate in an unusual manner (unlike a normal sotah), she is permitted to her husband who is a Kohen (and obviously then a woman married to a regular Jew as well). What's the chiddush (novelty)?
I would have thought that since she's deteriorating abnormally, even though she wasn't intentionally adulterous, we can say that she was raped while in seclusion with this other man. Since a raped woman is forbidden to her Kohen husband, this woman should be forbidden to him. The Mishnah teaches us that this is not true. But in what way is this not true?
According to the Mishneh LaMelech (Sotah 3:24), there are two ways to understand it:
If she was raped she would have died like any other sotah. Since she didn't, she must not have been raped, and is permitted if her husband is a Kohen.
The sotah water doesn't test for the case of rape. While it's possible that that's what happened, we aren't concerned for such a possibility.
The Toras HaKinaos gives a third explanation, that if she was raped she would deserve to deteriorate in an abnormal way. Since that's what happened, maybe it's proof that she was raped (and would thus be forbidden to her Kohen husband)...comes the Mishnah to teach us that this is not a proof, as it could just be a coincidence.
So you see from here that the default position of the Gemarra is that a sotah would not die if she was raped, and would be permitted to her non-Kohen husband. According to explanation #1 of the MLM, she would actually die (seemingly like the Maharal and Penei Yehoshua). According to explanation #2, she would not die, as the sotah waters don't test for this case. This is also the opinion of the Yerushalmi (Sotah 4:4), codified by the Rambam (Hilchos Sotah 3:24). It's also Rashi's understanding of the Bavli (32b). I didn't check if others understand differently. According to the explanation of Toras HaKinaos, she also would not die if she was raped.
In fact, the Toras HaKinaos, asks from this Gemarra on the Penei Yehoshua, that if she is treated as an intentional adulteress, why doesn't she die when she drinks the sotah waters? You see from his question that he doesn't see room to differentiate between the two (See also Yad HaMelech Sotah 3:24).
He answers that the case of the Penei Yehoshua is where she intentionally went into seclusion, and was subsequently raped. However, the Gemarra is discussing a case where she was coerced into the seclusion as well 1 (my guess is the witnesses aren't aware of the coercion, but I may be wrong). This would mean then that he holds that in the Penei Yehoshua's case, she would indeed die if she drank the sotah waters.
See also Tosafos Shantz to Sotah 6a, who says as a blanket statement that if a woman had consensual seclusion with a man, any resulting activity is considered consensual as well.
Sources culled from Oz VeHadar's Mesivta Shas.
1 This is how the Oz VeHadar Mesivta summarizes his words, but looking at them myself I'm not sure if this is what he is saying, I'll have to go over this again.
