Ted Thompson lacked experience in the 3-4 as a GM. But, he did play LB in the 3-4 for 10 seasons in the NFL. And he played under Bum Phillips as a 3-4 LB at SMU. So the 3-4 wasn't a completely new experience, as it is to Rick Smith.
The discussion is concerning Rick Smith's comments regarding the newness of the 3-4. Had Smith said, "The 3-4? No big deal, it's not so different", as you have suggested, then we would be having a different discussion. But, it was Smith himself who initiated the concerns of his lack of knowledge regarding the defense.
Rick Smith was around the 4-3 all of his collegiate and professional life. And he still failed to bring together the talent required to build a successful 4-3 defense. It's understandable how some are now concerned in regards to his ability to put together a defense he has never worked with prior.