I think a lot of people have ascribed
similar motives to Eccleston, in the period when he refused to say anything and all anyone could do was make wild guesses (or accept ignorance, but when has fandom ever done that?). But I don't know that he's ever suggested he felt a mainstream, highly visible role was inherently undesirable. He takes on material that interests him, or that pays the bills so he can do the stuff that interests him.
On the subject of the anniversary special, I don't think he was ever likely to appear in it, given that a nostalgic event episode in which he's one of three lead actors is unlikely to offer much if any new and interesting dramatic material. His turning it down (if he did; I'd remind people that the original article behind this thread, despite misleading wording, cites an unnamed BBC source rather than an official spokesman) probably isn't a comment on the plot.