He got work in the US. That's hardly having his career destroyed and is something a lot of UK actors are after. His comment about being blackballed sounds like Eccleston either jumping to conclusions with no evidence or trying to make excuses for his work record. In fact judging by his work record, he's had more major work AFTER Doctor Who, a lot of it at the BBC. He's a great actor, but he rarely commits to a job that requires extended involvement, is utterly miserable and complains about a lot of the jobs he's had. On top of that he likes to think the "elites" have it in for him because he's from the north, while other northerners have no problem.
I get the impression, from various interviews he's done, that he likes varied roles and wants to avoid being "stuck" with a role. Unfortunately no one explained to him when he took on the role of the Doctor, that he would be the Doctor for the rest of his life (Tom Baker finished his main run in the show in 1981. 37 years later he's still "The Doctor"). On top of the apparently bad working environment, I think this is his main issue, that Doctor Who tends to overshadow his other work (not unlike Sir Alec Guinness, who grew annoyed that he was mainly remembered for Star Wars, rather than the many other roles he'd played). His complaints about GI Joe and Thor seem to revolve around his dislike of franchise movies (and in the case of Thor it's probably warranted, given that the make up and direction prevented any sort of real emotive performance from him). He seems to have taken those roles without realising what they would be like and he's clearly avoided such roles since. It looks like he considers himself a character actor and dislikes being tied to any individual character.
Well, Tom Baker is also a genuine space alien, which I think contributed to his typecasting. I think Matt Smith also has such a distinct look that I think it might hamper his post-Who career in a way that it hasn't with Eccleston or Tennant. But it's hard to imagine Eccleston going into it without having at least some idea of what he might be in for considering that nearly every Doctor from Troughton onwards has worried about it to some degree or another. (Ironically, Doctor Who was actually how Hartnell escaped the typecasting that had plagued much of his career up to that point, since he'd previously been playing a bunch of gruff drill sergeants and gym teachers.)
Smith, I think, will probably find himself a niche in TV (I thought he was great in The Crown and he was the reason I started watching) whereas Tennant and Eccleston seem to have developed into a mixture of movies, theatre and TV (although Eccleston's comments on his roles in Thor and GI Joe may have cut back his options with major studios). McGann seems to have built a solid career too. Unfortunately the classic series actors were from a period when there was a fairly sharp delineation between TV and movie actors with very little crossover. You're right about Hartnell, prior to Doctor Who he'd been pretty much typecast as drill sergeant nasty and the role of the Doctor was very much against type for him. Although I think the original intention was to have the Doctor be a much less likeable character than he developed into. The unaired pilot contains hints of this.