@daemonguy I agree with your reasoning on why Haibara is happy and on that Haibara truly doesn't have any romantic feelings for Conan (at least as of this chapter).
I would like to add that Haibara is happy also because she has verified Conan's love for her (not the romantic type, but the companionate type) as she does for him, that even if Conan permanently turns back into Shinichi, defeats the BO, and gets the happy ending with Ran, Conan will still be committed to his relationship with Haibara, which she couldn't have been assured during the Pisco case yet, as Haibara still had doubts of Conan's character at the time.