Second: The fact that the votes were there on October 16 doesn’t mean that the votes were there on October 1. The reporting on this is murkier; there were enough Republicans publicly committed to vote for a clean CR to provide a majority (along with all the Democrats), but those same Republicans were not willing to side with Democrats on procedural votes which would have allowed a clean CR to come to the floor, so their real commitment to their public position at that point remains unclear. Some Republican did complain, either on or off the record, about the strategy they were following. However, reports from House Republican conference meetings up until the last few days tended to stress unity, and even enthusiasm, for whatever their latest scheme was.
To put it another way: The “Hastert Rule” is just putting a name on commonplace fact. Speaker is a party job, and of course the speaker is going to do what a strong majority of the party wants. It’s just that “what the party wants” and “which way they vote” aren’t always exactly the same thing. And, yes, speakers do have some tools that allow them to influence the votes of party members, but there are severe limits to that influence. Members of Congress, at the end of the day, are independent, autonomous politicians.
We can’t know for sure, at least on the evidence we have right now, whether Boehner was following the wishes of the majority of his conference on October 1 or on October 16. But what evidence we have strongly suggests he was. There’s plenty of blame to go around for the shutdown and debt-limit fiasco, but any account which focuses mainly on Boehner is probably letting both the moderates and the mainstream conservatives — in other words, most House Republicans — off far too easy.