See, here's the thing; if you actually watch the shows Seth does you'd already know that he actually loves the show - generally you have to have enjoyed and understood the original material to spoof it so accurately and scathingly - so worrying that he's going to go all "Family Guy" on it seems wrong headed. Also note that, despite the two follow-up series that were basically cash-ins on Family Guy's audience, at least one key writer in that house went on to create and produce one of the most beloved, and funny, kids shows of the last decade so the place is not just full of perverted ADD sufferers.
The bigger question is whether or not what made The Flintstones originally successful can even be converted to current audiences and, as Jaime Weinman points out about Bugs Bunny, whether or not the TV Executives will even allow what made the show work in the first place get on the air or declare it "unacceptable" for "modern" audiences. While the issue that he points to as making Bugs hard to recapture is less true for The Flintstones, the reality remains that both these creations are huge merchandising and marketing empires - The Flintstones had branded "family" product right down to cereals and Vitamins well into the 80's and early 90's that was largely driven by perpetual reruns - that are beloved memories to people. There's going to be pressure to recapture that broad based family friendly appeal and that means that going all Family Guy on it - at least in the sense of pushing the "taste" envelope - is fairly unlikely. So, while I could see some quick cuts I suspect any "adult" humour is going to be on the more subtle level of what you'd see back here.
With Phineas and Ferb long since past the episode count where Disney usually takes a show out of production and strips it into oblivion, maybe they should look into luring Dan Povenmire back to run the writer's room. One can dream, right?
Speaking of Disney... seeking to trademark "Seal Team 6"... really? Beyond the opportunism involved, how is that filing even possible? At a minimum, shouldn't the Navy already hold the rights to that and require licensing? At the furthest, how would the law allow one to acquire a trademark on a title that's seen use in media and content long before they gained their extra notoriety lately?