So in a world where there's microwave emitters and giant sonar devices, there's no room for a freeze gun? Even if Nolan had decided to use Mr. Freeze in B3, I really do believe that not only could he pull off a version of the freeze gun, but also a version of the suit.
Would Nolan provide a version of the character that was extremely close to what we see in the comics or BTAS? I think he would be faithful to the character, but I also think Nolan would attempt something new, both visually and how the character functions in story, the world, etc. We've seen Nolan take on villains in new ways, ways that have divided some fans (Ra's doesn't have Talia or the Lazarus Pit, Scarecrow doesn't wear a ragged suit with straw sticking out, Joker isn't perma-white) but have still remained faithful to who these characters are at heart.
I personally feel that what makes Mr. Freeze such an interesting character is his tragic turn moreso than his suit or weaponry, and that you could produce a faithful version of the character without having him wear the suit or having a freeze gun. I think Nolan would try to include those in some capacity, but I do believe the character can be portrayed faithfully without them, even if it did end up divided some fans.
But just taking the character as he is, he's not supernatural at all. His deformity is a freak occurance, and his suit & gun are products of science; ridiculous science, but as I said, look at the other occurances of ridiculous science in Nolan's films so far. In our world these ideas may seem improbable and preposterous, but even in the world Nolan has created this isn't impossible to achieve.
I think some of the worry behind this is A) how could Mr. Freeze be portrayed visually?, and B) how similar would Mr. Freeze be to the comics version? I personally don't even think about B) all that much for reasons I listed above, but A) is more interesting. Aside from The Joker, Nolan hasn't gone very theatrical with any of the other villains, but he did allow Two-Face to walk into clear view with half his face missing & his speech unharmed by the fire. Despite the visual faithfulness to the character, his deformity still comes across as ridiculous. I know some people have gone on about infections to Harvey's wound, but for the most part it's an aspect of the film that, despite its over the top visual, most fans love, including myself.
I think this speaks to what Nolan is willing to allow visually and conceptually. A man in intense pain with half his face missing can exist and function in his world, so why can't a man with frozen skin and a weaponized suit & gun exist as well? The science in this world is clearly there to support these weapons, and having frozen skin is no more ridiculous than mising half your face, especially in the manner Nolan showed Two-Face. Some people may dispute how this could be pulled off visually, but as I said in a previous post this is where creativity comes into play, being able to visually reinvent how these characters look and function in this world while still remaining faithful to who the character is at heart.
I strongly believe this is achievable in with Mr. Freeze in Nolan's films.