[Superkid11]

But every tv show has horrible episodes, stains on its underwear. I can think of a few terrible Stargate episodes (mainly the fillers from close to the end). And the old series of Doctor Who had some seriously crappy episodes didn't it? (though I am unaware of them)

Like I said, if RTD's bad episodes were damaging enough to effect the very core of the series then most of this season would have sucked. But it didn't, did it? You were pleased with most of it it looked like.
The other writers can bring it out of the darkness, especially now that RTD won't be in charge. Yes, those episodes can't be erased from canon, but it's not like they'll infect all the others. I apologize for my optimism, but I'm just going by what I've seen.

Unless there was some kind of mind blowingly horrible canon-changing event in this episode that WOULD effect future episodes.