It's not at all that it's a bad thing to read fanfic as original fic (it's weird to me, but that doesn't make it bad), except that if you do get into the actual show/book/whatever ... I would think it'd be a jolt, as you indicated. :) I do think whatever your original source, that's how you see the characters to a large degree, whether that source be the show, good in-character fanfic, or wildly OOC fanfic that makes you eventually think "what show was this writer watching?" when you actually see the show. :) (With, of course, the caveat that in character and OOC are in the eye of the beholder).