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I don't think any story should be excluded from a contest merely because of its length. It's not worth it to have a simplistic "no further or your story is ineligible" maximum word count rule, which limits everyone, just to help keep one or two writers in line - if their story suffers from major scope creep they should either exercise self-control for the contest's sake, or break it up into chapters.
During this contest it was the Under 5k category which ended up being a major driver of submissions, so rather than a maximum word count which seems to lead to discussions rather than fics, wordcount-categories sound like the idea to expand on. Something like Under 1k, Under 5k, Under 10k, Under 20k, Under 50k, Holy Shit