You can't have it both ways. You're either an encyclopedic website that seeks to be factual and informative while minimizing speculation or you're a fansite. Either way, it's not suitable for inclusion. For example, if your site is a community run information site, then it should not be included under the In general, any site that does not provide a unique resource beyond what the article here would have once it becomes an example of brilliant prose guideline. Your Wiki won't provide information we don't already have or will have in the future if its just a community info site. However, if it trades in information that we won't be adding, such as speculation, theories, spoilers, because of Wikipedia guidelines on such material, then we should not be posting your sites for the reasons discussed above. It is not the case of making a link between encyclopedias, but between an encyclopedia and one particular fansite.
Further, the two Wikis you mention aren't even major fansites, when the guideline specifically states: Fan sites: On articles about topics with many fansites, including a link to one major fansite is appropriate, marking the link as such. In extreme cases, a link to a web directory of fansites can replace this link. We already have the major AND official forum: The Fuselage. If you'd like to add a link to a directory of Lost fansites, be my guest... but inclusion of either Wiki alone (instead of a list) is preferential treatment of minor fansites, since there are certainly other, larger, more popular fansites (Lost-media, Lost-tv, for example). Certainly, if we were to start adding fansites at random, we'd have to begin there and with others, like a link to TWOP's reviews and forums. The best course of action if you believe these sites simply must be linked to is for you to make a list of fansites and include a link to that directory, which is how WP:EL says to proceed.
As for removing the disclaimer, its not going anywhere. The disclaimer was put there specifically because we'd have people posting each and every fansite they dreamed up as official sites when they weren't. Lost is an example of a show wherein Wikipedia guidelines and policies are repeatedly ignored by the editing community, so the long-term editors have had to be very diligent in monitoring this page. This is an outgrowth of that, and has for the most part helped a lot. Moreover, there is no "freebie" section for links. All links listed there are official sources except IMDB, which is used almost without exception. The same list of reasons I mentioned above for IMDB, including the fact that IMDB is a featured part of the standard TV Infobox, clearly do not apply to these Wikis nor any other site people have been trying to add (Mr. Clucks, 4815162342, etc.)
Finally, I will agree with you that the list of links for all the individual networks is redundant, and should be chopped down or moved to Airdates of Lost as a link for the country/network listed there.