I think he's worried about Elinor's wish that Marianne's idealism should be tempered by "a better acquaintance with the world." Marianne's currently acting on the principle that a true, sincere (first) love justifies any behavior, no matter how reckless or conspicuous or ungracious. Elinor thinks that it would be good for Marianne to be sobered up and brought into line by "a better acquaintance with the world." That Marianne would remain idealistic, but not to the point of being irrational or improper.

But Colonel Brandon fears that if "the world" caused Marianne to give up her "romantic refinements," they might be replaced with a much more harmful attitude of cynicism and worldliness. So he's warning Elinor that Marianne's "enthusiasm and ignorance of the world" are actually preferable to the state she might be in if she lost her idealism.

He's afraid that Elinor is taking a "tough love" view that it would be good for Marianne to pay SOME social cost for her reckless behavior and learn to be more rational/temperate about love (including admitting that a person could truly love twice). I think he sees Marianne as the kind of person who would be damaged by "a better acquaintance with the world" rather than benefiting from it; she would become cynical rather than rational.