She's scum. She feels like scum. Applejack knows she is pure scum, and she wants it to stop.
There's nothing wrong with falling in love with your best friend, but there's something definitely wrong with your head if that best friend is possibly your cousin. Well, distant cousin, but she's technically part of her family (possibly).
It's that possibility that's messing with Applejack's head. There's a possibility that Pinkie is not her cousin, but the option still exists. Applejack doesn't want to date Pinkie only to find out later they're actually cousins.
It's like you finding out the boy or girl you have a crush turns out to be your long lost sibling, or something.
Applejack understands that the 'incest' thing is a kink, but she doesn't like it. She's from a big family, and she can't imagine being in a relationship with any of them without vomiting.
Anyway, Applejackwants to stop this horrible feeling towards Pinkie Pie. She fell in love with her when they knew each other as friends. If Applejack knew that Pinkie was her distant cousin from the very beginning, these feelings would never have existed!
That's one of the reasons why she felt like scum. The second reason was... jealousy.
For a while now, Pinkie revealed that she has a boyfriend, Cheese Sandwich, which isn't surprising actually. They can keep up with each other, they love parties, they love each other, and Applejack was jealous. Jealous of Cheese Sandwich.
That made Applejack feel like she's the worst pony in the entire world. She can't be happy with Pinkie's perfect relationship because of her selfishness, her disgusting selfishness.
What is she suppose to do about this!? Who can she even talk about this?!
She knows that Big Mac fell in love with Marble, but at least he only knew her for a little bit, at least it was just a crush, and at least he found Sugar Belle. For Applejack, she knew Pinkie Pie ever since she've moved to here in Ponyville, and Applejack fell in love with her passion for others and their happiness. Of course, Applejack can be annoyed by Pinkie's antics sometimes, but that's just a small part.
Applejack hoped that maybe some other pony would come along and catch her eye, like Sugar Belle did for Big Mac, but it haven't happened yet.
If it wasn't for the fact that Pinkie might be her cousin, Applejack would happily ask her out, but she can't. It's the chance of hitting that taboo Applejack is afraid of.
She's happy with being friends with Pinkie, but she wants more and she can't have it.
And so, until the day they find proof they're not cousins, Applejack can't be honest with her feelings.
AN: So... This was a result of realizing that I want to do the Mane 6 x Mane 6 little project thing, but then I realize that Applejack and Pinkie are possibly distant cousins, and that's how this angst-y mess is came to be. I want to be clear that I don't like incest at all, but I won't hate people who has it as a fetish (I might have second thoughts if you think incest should be a normal thing. No offense(?)).