I'm upset it happened to Conan, but you're right, he'll be better off being able to be "himself" and not trying to conform to The Tonight Show format.
Comedian Louis C.K., who used to write for Conan, expressed the same thing. He said something like "I don't understand why Conan even wanted to host The Tonight Show, which is geared towards baby boomers, when he has Gen X and Gen Y s his following."
He went on to talk about how Letterman, and then Conan had actually built their own "brand awareness" thru Late Night. People would say "did you see Letterman last night?" and then "did you see Conan last night?" They had become the brand.
Edited to add:
I found the article
http://www.vancouversun.com/entertainment/Shock+comedian+Louis+says+Conan+Brien+gave+first+break/2472481/story.html