I agree, Rogue and Ninja are complete different cultures.
I think the initial goal was to create a Ninja mixed with Eastern and Western techniques. But in the end, it just became Ninja.
Rogue/Thief doesn't have a good representation in the game beyond being a class. Thief was actually a job with characters to represent it, Locke from VI or Zidane from IX. Last one is a bit more fantasy magic thief.
In any cases...

SAM is your best choice to go. No big madgery, just sword swoosh and low positionnals count.
MNK has a lot of positionnals, it's the identity of the job. No magic except Chakra thing and punches.
Dragoon is heavy armor but you can glam light armors.

Other than that, Tanks and ranged are the non-magic jobs.