I would highly doubt that she could be in trouble for not already declaring him. You two aren't legally married (military and DOD don't really give a shit about common law) and she hasn't met him. Besides, I'm not sure what clearance she has? Do you know? If she is in intelligence and has a TS, it is possible she might get a raised eyebrow for not having declared it before, but that is probably because they'd be incredulous that she claims to not have met him before.

If she isn't in intelligence, then it isn't surprising that she hasn't any clue about Personnel Security, in which case, she needs to seek some mentorship on the topic. And if I were you, I'd let her know that it would absolutely be in her best interests to declare him when you're married and be told Security doesn't give a fuck than to not declare him and get caught later on. That is when Security gets suspicious.

So go get yourself married. Be super happy. Don't jeopardize his citizenship/visa/whatever the hell it is you're doing, by not getting married. You aren't screwing your sister over, regardless of how dramatic she is acting or how uninformed she is about this topic.

As an aside, I wonder if you're not being a bit obtuse, though, about her feelings and your relationship, because I do think it is reallly really really really weird that you guys are so close but she doesn't want to see you. Is there something about her that she wouldn't want you to know? Like, does she have a black eye because her hubby is beating her and she knows you'd go spare if you saw it/knew? (I'm grasping at straws here, because I don't really know of anything that could cause this reaction from her other than either a hugely inflated opinion of the sexiness of her job or ignorance of this well-established process.)

Hope it all works out for you.