Random thoughts:
It seems to me that there might be three sets of issues preventing the non-chasidic rabbonim in the US from addressing the issues:
1. As you have noted, they are not willing to do anything that would involve subjecting R' Shmuel to any amount of criticism. I think these people could be divided into two groups.
a. There are some who want to protect R' Shmuel because they believe that anything he does is necessarily correct and that to question him is to question Hashem. Therefore, if R' Shmuel was involved in the heter, no one has the right to question the heter.
b. There are some who want to protect R' Shmuel because they believe that he is an important gadol who has devoted 70 plus years to serving the Jewish People. They are incapable of accepting the possibility that R' Shmuel did anything wrong. They believe that R' Shmuel (1) either has absolutely nothing to do with the heter or (2) at most they are willing to accept that R' Shmuel made an honest good faith mistake in being very peripherally involved in the heter. But they are unwilling to even entertain the belief that R' Shmuel either (1) was substantially involved in the heter, (2) would have any part whatsoever in advancing the heter in any possible fashion (including not objecting to the heter) if R' Shmuel had any doubts about the heter's validity [in other words, they believe that R' Shmuel was at most, peripherally involved in the heter, and that if so, he honestly believes that the heter is completely justified], or (3) wrongfully intervened in this matter in any fashion on behalf of a family with whom he has longstanding and extremely close personal and financial ties. It appears to me that even Rabbi Feldman and Rabbi Miller fall into this category.
2. Even if R' Shmuel did something wrong, exposure of this fact would somehow degrade respect for "Daas Torah" and respect for the "system." In short, they fear that transparency itself is harmful.
Within this category, (a) some believe that exposure of any wrongdoing or misconduct of whatever sort is generally bad, and (b) there are some who have a vested interest in a system whereby insiders, in which those who are wealthy, related or just well-connected, receive favorable treatment from the system - which in many cases doesn't involve other parties necessarily ending up on the losing end. They are unwilling or unable to disconnect the concept that a rich donor will receive attention and honor for no real reason other than that person being a rich donor (which is a reality, and oftentimes completely innocent, but something they might not want to acknowledge), from that bleeding over into such type of person getting an unfair advantage from the "system" when such person is involved in a dispute with a "plain" person.
3 - a Those who believe from a moral perspective that a woman is necessarily entitled to an unconditional no-questions asked get upon demand no matter the circumstances. They are therefore extremely uncomfortable with a situation where halacha results in a woman not being able to get remarried under halacha, and therefore willing to try to "bend" halacha in order to achieve what they see as the morally correct result. These people have adopted the general moral norms now prevalent in the U.S. that have their origins in the radical counter-culture of the 1960s. Some of these new moral norms generated by the counter-culture have seeped into even the most yeshivish parts of the Orthodox world. No-fault divorce against the will of either spouse was not available in any U.S. state before the counter-culture, but is now available in every U.S. state - and now seems, at least to many in the Orthodox community, to be the obvious morally right answer. Other norms of the counter-culture may not have yet been adopted by the yeshivish, but have started seeping into more left-wing parts of the Orthodox community as well, such as the Open Orthodox attitude towards gay marriage.
3-b There are also many who believe that 3-a is the position of the masses and that the rabbonim have no choice but to go along.