The problem with your question is that it makes no sense; "going too far" doesn't mean ANYTHING, especially in the context of a work of fiction. It could mean too far in terms of ratings (such as highly violent material in a work aimed at young children) or in a legal sense (actually attempting to publish and receive money from fanfiction is the only way I could conceive of it going "too far"), but otherwise the wording is perplexing. Fanfiction can certainly be bad, both in general writing skills and any buthering of the source material (Sturgeon's Law applies to fanfiction same as anything else, though it appears moreso because there isn't any screening process), and on rare occasions can cause spontaneous bleeding from the eyes, but there isn't much cause to worry about it "going too far".
Slightly relatedly, I laugh both at the myriad of people here who dismiss all fanfiction entirely, as well as those who go straight to the typical "warnings" of things like My Immortal, Cloud Mows the Lawn and Full Life Consequences as if they A) aren't obvious troll fics, and B) are in any way representative of fanfiction as a whole. I can't remember all of the fanfiction I've read that was not only a wonderful representation of the setting but quality pieces of literature in their own right (which I won't list because I will probably be here all day), which goes back to your original concerns about writing fanfiction.
It's just like everything: it will only be a serious work if, first of all, it is treated like a serious work. If you only view it a fanboy's fantasy, then that's all it will be. If, however, you view it as a work of which you can be proud that only happens to be derived from a fanboy's fantasy, that's what it can be.
