I'm under the impression that back in the 2005 relaunch there was a strong gay quotient at the top of the chain (Davies, and I think Collinson), Barrowman was chosen very deliberately to fulfil a desired representation in the series, and I am not sure whether he was already friends with the two, but regardless of that the reality of the working environment was just that - if you were on the show as a jobbing actor or crew member you would have been aware of this reality and been very cautious about raising the issue... I do think that is why Barrowman was so fearless in doing what he did, any other show and the conditions would have been different and the management at the top not tolerate such behaviour.
In the end that is what it came down to really - the culture that was generated and enabled by the people at the top. And Barrowman feeling very sure he would get away with it because of that, and who was at the top.
The fact that Barrowman had more job security than an actor with a bit part or crew member is true no matter who was at the top. Captain Jack was a big part of the second half of series one, and perhaps from the beginning there were talks about doing more with him. People who feel replaceable are not going to rock the boat.