They are/were, even by the EU's standards, fitting that Nazi-motif. The EU just slipped in that Thrawn and his species have a slightly higher level of acceptance, and while most Chiss don't rise to that kind of level, Thrawn was able to because of the man he was.
If you're sticking with the Nazi thing though... Even the Nazi's relaxed their rules as to who can be in and who can't. There were SS regiments formed in conquered territories, there were men in the upper echelon of the Reich who didn't believe in the Nazi ideals but who were just good soldiers. Many of them died on this very week (Operation Valkyrie), actually. I've always viewed Thrawn as the Erwin Rommel of the Empire... Educated, intelligent, not always an insider with the Nazi party but a valued officer, and one who saw the faults of the Nazis themselves, and that they were simply bad people.
The only thing I don't like, which I mentioned, was THrawn's place as a GA too early. If they'd had him at a lower level like his EU story played out, I think it'd make him even more threatening because you could play his ambition card... As a GA, Thrawn is really pretty close to Tarkin but in separate branches more or less. I'd have liked to have seen things done differently but the show's rumored to not last as long as TCW did and so maybe they're not wanting to get too complex with names/titles and stuff.
They kept a lot of Thrawn's background though. His studying his enemies, his art collection, etc. They're wanting that element the Thrawn Trilogy had of Thrawn being just as deadly and threatening as anyone, but without force abilities and just a purely strategic mind. I love that.