No, it's Keith Boak he didn't get on with.
The issue went up to the producers, hence his quote about people "schmoozing at cocktail parties" while people on set were treated poorly.
Eccleston has repeatedly said that The Empty Child 2-parter was the best script he was given though so maybe he'd be up for returning if Moffat was behind it. Doubtful but weirder things have happened.
The cocktail parties line was in reference to the difference between acting for adults and children - it's not clearly a reference to the conditions on Who at all so you're making a big assumption there. No one else seems to have had an issue with the amount of work that Collinson or RTD did.