Rondo asked, but didn't receive permission and stayed anyways. It's pretty logical.
I understand why you're making that inference, but I'm not sure that that conclusion follows from "Rondo did not receive official permission".
That could mean, as you suggest, that he was denied permission. It can also mean that he didn't receive permission because he didn't ask. Heck, it could even mean that he didn't receive "official" permission, but that he'd received some other sort of "unofficial" permission. That last one doesn't make much sense in context, but it's an example of what we can infer when we parse a reporter's words closely.
There's no need to parse, Bulpett explained it pretty clearly last night on WEEI. The problem wasn't that Rondo stayed behind or didn't inform the team he wasn't going to Sacramento. The problem was that he "told" them he wasn't flying to Sacramento instead of "asking" whether he could stay behind.
The gray area that Bulpett spoke about in his article is two-fold: first, under Doc Rivers if vets weren't playing on a road trip they were given a choice of whether to travel or not. They didn't have to ask permission--it was their call. Second, asking permission was just a formality anyway, since the answer is always "yes". So if you know the answer before you ask sometimes you just don't ask in the first place you just tell them you're doing it.
So Rondo got lax with protocol and Brad got a little upset because the impression from the outside looking in is that Rondo is dictating things to his coach and not the other way round. Hence the talking to and the possible fine.
The actual incident isn't much to talk about, but the context of the incident is. Even the fact that this got out is kind of indicative of the state of that locker room right now. What happens in the locker room should stay there and when it starts coming out it's usually a sign of discord. Brad or the coaching staff were the source of this leak and even then the sources Bulpett reached out to to confirm the story disagreed amongst themselves as to the severity of the breach of protocol. Brad obviously felt he needed this public to keep his locker room in order and/or to send a message to Rondo. We'll see if it worked but airing things in public is often a last resort (or it should be)--and I'm sure Brad understands this.
It's also pretty clear that Ainge and Rondo need to have a talk because both guys have been pretty tepid in their support of each other in the last week. I don't think Rondo likes the no back-to-back rules, the losing, or having his name in trade rumors, and whether it was intentional or not he kind of acted out in this instance. Danny for his part in this last week has been as unenthusiastic about Rondo as I've ever heard him. Usually after rumors pop up he goes out of his way to prop Rondo back up--this time he didn't, and instead said he expects that in the summer there will be better offers.
I hope Rondo stays around long term but this last week has shown there to be some cracks in this relationship. They can be mended but I can't help but wonder if Danny had just done the smart thing and said that Rondo was unavailable at the trade deadline if this all could have been avoided. He was never going to get full value at the deadline for a player coming off injury and all he's done by listening to offers is depress his greatest asset and upset his best player. Not the smartest move considering free agency is 16 months away and they're going to try to get Rondo to take a discount to stick around.
The only times Danny has lost a free agent has been when he's disrespected them (see TA and Ray Allen). It's never been about money, it's always about respect and I fear if we lose Rondo that's going to be the contributing factor. When's Danny going to learn that you need to show a little love, respect, and loyalty to your players when you demand the same thing from them?