Confessions of a Liberal Puritan

Yes - and in AYW, which is actually a better episode than many of us give it credit for, does show how Riley's changed. Note - he does not tell Buffy how to handle Spike nor does he cart Spike off or apprehend him - even though it's clear that Spike was the person he was hunting. Later, he tells the operatives in Sunnydale that when it comes to Spike to defer to Buffy. This a huge change - and it is one that began in "New Moon Rising" - when Riley has a sort of Epiphany, he realizes Buffy's right, he is being prejudice, that the universe does not fit into neat little boxes. But he struggles with the notion - as we see in Yoko Factor. And Buffy, to give her credit, understands that struggle - because she's faced with a similar challenge when she finds out Willow is in love with Tara - which momentarily gives Buffy wiggins, as she puts it.

The theme of order vs. chaos is consistent in all of Whedon's tales - from BTVS-Firefly. And he explores the negative and positive aspects of both. Wolf Ram & Hart symbolize order in Angel's universe, Jasmine is a demon of order, yet the Beast which brings her into fruitation - chaos.
In Buffy - we have the Mayor, obsessed with order as well as Adam, while on the chaos side - Angelus/Spike/Dru/and to an extent Glory. The First Evil and Caleb represent both. In Firefly - we see it represented in the "Alliance" vs. "The Reavers", with the crew of Firefly representing the middle ground.

It's a problem in many religions, I think - finding that balance. Knowing when to control and when to allow people to come to their conclusions. The difference between dictating and guiding, because God does not dictate so much as guide us, if God dictated there would not be free will. People think that if you make everything orderly, structured, evil won't exist. (Recently I had a conversation with someone who actually said Hitler had the right idea, he was a good leader, because he imposed order. Dictated how people should live their lives, that we should not have free will, and indeed have too many rights. So lives were lost, at least everyone had a job, food, shelter - much like Connor's justification of Jasmine - so people are eaten, at least everyone's happy. But there's no art, no creativity, and free will is gone. Many religions state the same thing - they dictate.)

Have you read Phillip Pullman's "His Dark Materials"? It is in some respects a counter-argument to the Christian beliefs of CS Lewis as depicted in the Narnia novels or the view of an "orderly" world. In it Pullman appears to state that without free will, we have nothing. That being controlled is worse than death. Whedon states the same thing. Yet, if we have no rules, no order, no structure - we will destroy ourselves. There has to be a middle ground.

The fight between the two extremes isn't just in religion, we see it in economic systems and government infrastructures. Anarchy on one side - Tolitarianism on the other. The systems that survive the longest are the ones that discover a middle ground.