Family Guy becomes just another one of those short-lived cartoon series that some network tried to copy the Simpson's with. Because the creator was on one of the planes on 9/11, it gains a bit of a cult following with videos and syndication. People who worked with McFarland get to call him a 'genius' who died before his time, and then use that connection to get some good gigs.
Fox might try another animated series on next to the Simpson's, maybe another Groening project. Don't know what the results of it is, but I'd see two possibilities: they hit upon a successful show that caters to the same audience as Family Guy OTL, or they fail and that audience finds something on cable instead. Today, we see a slightly different TV lineup on Sunday nights, some different internet memes, etc. But not many other differences.
Although, it'd be interesting if Fox decides to try something else instead of an animated series if they continue to fail to find a good one. How about they try to come up with a replacement for the X-Files, which is dying around this time, and sink some money into a new sci-fi series to replace it. They can compete with Alias, maybe look at attracting the Buffy audience, without looking like a direct copy of either... hmmm... would Firefly do better on Sunday nights?