Hah, excellent! I wasn't sure how you were gonna deal with the whole Philosopher's Stone thing, but Harry (more or less) accidentally getting through all the defenses was just perfect, and completely in line with the rest of the story, so it worked out great! I can't wait to see Harry reaming out Dumbledore in the next chapter! :D
Since you mentioned two possible options for the "future", my opinion (for what it's worth) is that you should stick with option 2. As fun as it is to read a little canon-bashing once in a while, once it becomes gratuitous, I tend to get sick of it really fast, and I'm afraid that you'd cross that line if you decide to stick with canon (while ignoring the logical consequences of the differences you've introduced), so I hope you decide against that. Also, there are already way too many stories that simply rehash canon, and if I wanted to read that, I'd pick up the books again, instead.
But one thing worth considering (if you actually want to include him), is that Lockhart had (most of?) the Wizarding World completely fooled, so it's not too unlikely that he'd still be hired. Of course, how long he'd actually last once his incompetence became clear, is another matter entirely... ;)
Perhaps he could pour some kind of potion that tasted like an easily recognizable poison into Snape's drink and cause the man to have a mental breakdown.
YES, please! I'd almost pay money to see Harry do something like this in a later chapter, so I hope it was more than just a random thought! :D Of course, actually poisoning him would be even better, but since he probably carries around 362 different poison-cures all the time (with his personality, you just know that people try to poison him on a weekly basis...), messing with his mind would definitely be a better solution, not to mention a lot funnier.
Oh, and as far as the last part of your rant is concerned (Harry burning Quirrelmort), I hope you don't mind me sharing my own thoughts and conclusions, again. Because as far as I can tell, that was actually adequately explained in Deathly Hallows.
When Lily Potter sacrificed her life for Harry, she gave him the same kind of "shield" or protection that he gave the entire Wizarding World at the end of DH; namely one that protected him from Voldemort. It gave him protection from any directly harmful actions, and thus, the AK rebounded (and other harmful spells would also be less effective), and any physical attacks would hurt (while the jinx on the broom worked just fine, since it didn't directly affect Harry).
So, in a way, the whole "it was your mother's love"-thing isn't entirely accurate, since it was Lily's self-sacrifice that actually protected him (until Voldemort bypassed that protection by using Harry's blood for his rebirth), but it's not completely inaccurate either, since that kind of selflessness almost necessarily requires some kind of love; in this specific case, a mother's love for her child, leading to her putting his life ahead of her own.
So if you want to criticize anything, I'd focus more on the in-character acts of Dumbledore, actually, since he was speaking in riddles as usual, and using flowery words to cover up his unwillingness to actually explain anything (also known as "bullshit").