I think the prequels contest perspectives of the Force through failures in the current mainstream Jedi philosophy, which is not necessarily either entirely their fault and/or that there are not instances (like this one with Mace Windu) that prove the standards of the Jedi were to high and need to evolve...
OBI-WAN: Don't defy the council, Master, not again.
QUI-GON JINN: I will do what I must, Obi-Wan.
During The Phantom Menace viewers come to learn that Qui-Gon Jinn is somewhat "rogue" in terms of how he feels about the nature of the Jedi Order and its Council. This prompts three lines of thought going forward...
- The Jedi Council indicates a hierarchy within the Jedi Order.
- The Jedi in part fall, because they resign from peace-keepers and become soldiers of the Republic, because The Council believes they should work with The Republic.
- That although it is easy to blame Jar Jar Binks as the bigger screw-up in Attack of the Clones, the truth is that Qui-Gon is the one to bring Anakin into the realm of the Jedi Order, claiming him to be The Chosen One, and Anakin is apart of Palpatine's grand plan.
With these ideas, one can see the general problems with the situation in a broad way, but it also contest's Qui-Gon Jinn himself, being someone who was right in the sense that the hierarchy structure and commitment to the Republic is not fair or a good way to approach doing good work on behalf of The Force, but yet he couldn't foresee Palpatine's plan and brought Anakin into preview of the Jedi Order.
However, when one looks closer at Anakin's fall one can also see some discouraging or hypocritical things coming from The Jedi directly...
"Attachment is forbidden. Possession is forbidden. Compassion -- which I would define as…unconditional love -- is essential to a Jedi's life. So, you might say that we are encouraged to love."- Anakin Skywalker, Attack of the Clones
- Personal Attachments and Possessions are Forbidden, but in truth the Jedi raise younglings and train Padawans, in which a master and apprentice have powerful bond (Obi-Wan thought Anakin "a brother"), and as Obi-Wan states: lightsabers are a Jedi's life.
- The force visions and concern for his mother were not inaccurate. He might of been able to save her life. The act of being able to do so, may have caused him less pain.
- Fear is seen as precursor to the Dark Side according to Yoda in TESB/TPM. But every film of the prequels there is an older Jedi who contests and fears Anakin. Yoda fears his fear and doesn't want to initially train him (TPM), Obi-Wan doesn't trust him, but Yoda tries to mend his former reactions towards Anakin by reminding Obi-wan that being older doesn't mean you are better (AotC), and then in Revenge of the Sith Anakin is on the council, but denied the rank of Master, despite that he fought well and took on an apprentice during The Clone Wars, The Council wants him to spy on his friend, and Mace Windu flat out says he doesn't trust Anakin.
- The Temple on Couroscant was somehow unknowingly built on top of a Sith shrine clouding everyone's judgement and probably enhancing fear and paranoia.
So going back to this scene with Mace Windu, one could say that, yes, he went against the Jedi believe system by not wholeheartedly following "due process"and being "encouraged to love" and in affect, the action of wanting to kill Palpatine this way is how A JEDI would believe a Sith would act, but at the same time, despite what Anakin didn't understand about what Palpatine had done, is still understandable and might have been the right thing to do since most likley with Palpatine, it would have been "kill of be killed".
But in addition there is new information coming from the ongoing Darth Vader comic series, that turning to the dark side is not instant, but an ongoing process, as Vader has many trials in attempts to quash his light, but ultimately during the latest arc, seeks to still save Padme' from death!
Mace Windu may have taken a step towards the dark, but it takes more than that to embrace the dark side fully in terms of the way we come to see Sith Lords do it.
So over all I think the prequel era is trying to tell us that the basic perspectives of the light and the dark or the black and the white views that the Jedi held were impossible to live up to without becoming Sith-like themselves, because of the way some their ideals alienated Anakin through fear and mistrust, hypocracy, and a lack of transparency, which is echoed through this tough decision Mace Windu was trying to make.
And lastly I would like to add these ideas are also within the current ongoing narrative of the sequel trilogy, as The Last Jedi's story with Luke becoming the centerpiece and important factor in Ben/Kylo Ren's backstory calls back to Anakin's behavior when he killed all the Tuskin Raiders (AotC) and all of the younglings at the Jedi Temple (RotS), but also then this Mace Windu scene, because the concept of morality in face of murder or assassination is the connecting theme and a juxtaposing scene.
"Let the past die. Kill it, if you have to." - Kylo Ren, The Last Jedi
To further this The Last Jedi also introduced the concept of 'letting the past die', which was first showcased in The Force Awakens when Ben killed his father, Han Solo. It comes up again when Kylo Ren couldn't take a shot at his mother's ship, feeling her through the Force.
"The Jedi must end." - Luke Skywalker, The Last Jedi
But it is also present in Luke's story, as he states a similar idea when he says, "The Jedi Must End". Both characters though are proven that the notion of letting the past die is false, because Kylo Ren is seemingly motivated by his obsession with Darth Vader and is pushed closer to Snoke with a series of interactions between Luke & Kylo calling back to Anakin's actions AND Luke finally redeemed says, "I will not be the last Jedi". The Jedi text also mysteriously end up on The Millennium Falcon presumably for Rey to find.
"I will not be the last Jedi" - Luke Skywalker, The Last Jedi
So all of this is pointing to ideas that the Jedi philosophy needs to evolve, as oppose to parish and this Mace Windu's scene is one indication of this by purposing a grey area in terms of how Jedi have viewed themselves and the Sith.