House Elves
My theory - not very original, as someone else suggested it here too - is that the Apparition ban at Hogwarts covers spells, as cast by wizards. House Elves cast no spells. Their Apparition is an innate magical ability. In DnD terms, House Elves would have (Su) Teleport Without Error in their description. Wizards, on the other hand, have the spell on their list, which is much different.
R.A.B.
Amelia Bones... If I recall correctly, she oversaw Harry's trial. Thus, she was not dead. The locket that Harry recovered mentioned that R.A.B. knew that death was coming, and pretty quickly, too. Also, it can be assumed that R.A.B. had Death Eater connections, due to his knowledge of Voldemort, and because non-Death Eaters or sympathizers don't tend to refer to him as the Dark Lord very much. So, I'm fairly sure R.A.B. is someone who betrayed the Death Eaters. I hadn't thought of it myself, but my own niece's theory is that Regulus (A.) Black is the one responsible - again, something already brought up here.
Snape
There are AMPLE reasons provided already, strongly implying, if not proving, that Snape is one of the Good Guys.
Floo
The Floo Network can be connected, disconnected, monitored, and otherwise controlled. I think it's safe to say that a massive invasion of Death Eaters going to Hogwarts via Floo would be intercepted, and probably not in a very pleasant way, even if it was connected.
Harry at Hogwarts
I'm fairly sure that Hogwarts will play a much bigger role in the seventh book than Harry suspects now, at the end of HBP. Not only does he lack the knowledge to begin hunting for Horcruxes on his own, but I remember the description of the series that I read, ages ago: the Harry Potter series shall consist of seven books, one for each year at Hogwarts. Besides, abandoning it now will have the seventh book resemble the first six even less than it will already - even assuming he goes, he won't have the traditional antagonistic from Draco on the Express, the glaring of Snape and the speechmaking of Dumbledore at the first dinner, etc., etc. It won't be Harry Potter if he does as he plans at the end of HBP - the book would not be recognizeable as part of the series. Already, I'm dreading the mopey beginning of the final book. (Also, if the school year at Hogwarts was unimportant, why would the series be limited to seven? Why not ten? A dozen? The remnant of Harry's battle against the Dark Lord seems like it could be stretched out to an awful lot more time and money, were they so inclined.)