I haven't given much thought on that particular scenario, mainly because I have a new PLL code now, and that is if something gets too far behind (such as the Ali funeral scene), it probably won't come back into play because the writers forget a lot of things.
But about 6B, I'd say I believe somebody made sure Charlotte was released so he/she could kill her. He/she convinced/blackmailed Mona into "demanding to be heard" at the hearing to ensure that Charlotte would be released, and that is why Mona was acting strange both at the hearing and at the funeral, storming out both times.
Now, I pretty sure they're going to recreate "That Night," making it out that Charlotte had met up with a billion other people before her death, so it's possible that she met with Ezra and other people before her showdown with her murderer.
If we're going the murderer isn't Uber -A and Uner -A is an avenger route, then I'd say the murderer is one of these people:
*Elliot Rollins: for reasons unknown or to simply parallel Vertigo, as others have already mentioned on this sub.
*Melissa Hastings: to protect Spencer once again from the threat. I highly doubt it though, because Melissa was devastated for "killing" an "already dead" girl, I can't see her being capable of murder in cold blood and showing up all bubbly in 6x13. Also, I personally believe she had an interesting relationship with Charlotte, so hopefully the writers touch up on that.
*Sara Harvey: simply because she seemed to hate Charlotte's guts. But honestly, the whole "she's here to make sure Charlotte's dead" makes it seem like somebody else killed her and sent Shower to check up on her. Hopefully this is the case because I want this terrible character out of the show ASAP.
In all the cases above, whoever turns out to be the murderer, I think Uber -A would be either Melissa or Alison.
However, if we're going the murderer is Uber -A route, then it's probably:
*Melissa Hastings: we still have no idea what kind of relationship she and Charlotte had and it could hace easily been a toxic one. I hope we find out.
Alison DiLaurentis: this is my all-time favorite storyline, to have Alison be as bad as she is in the books. I have no basis for this but honestly, her "redemption" arc turned her into one of the most boring characters on TV. I think I speak for the majority when I say I'd rather have her be a villain and not get a happy ending over her being a grandma cleaning laundry and setting tables till the end of the show. This would also be great a callback to [spoiler](s/ "Alison murdering her sister in the books.") Better late than never, right? Though I have no reasons to base this on yet.
Of course, my thoughts might all change as more episodes air, so we'll see how it goes.