The Guardian has another article about on-set behavior. It seems to be a big reason why Eccleston left (that, contrary to popular opinion, he enjoyed working with Davies and Piper, but he had to defend others on set), while Tennant had the effect of making the set more grounded and professional.
And not to defend anyone, but the BBC said they reprimanded Barrowman about his behavior, which they said he then promptly stopped. I think it's telling that while Clarke has these allegations, revelations about Barrowman aren't from past on-set colleagues (though that could change), but rather pieced together from comments by other actors during conventions, Q&As, and even parody songs by the cast that poke fun at Barrowman. If Clarke was reprimanded but continued in this behavior, then yeah he's in even bigger trouble.