Note that on the Wikipedia page for Chris Slowe [3], another person who joined Reddit very early on, he is also described as a co-founder, but he doesn't appear on the About page, even though there's been no public falling out between him and Steve/Alexis (he stayed at Reddit post-acquisition, then jumped to Hipmunk with Steve, and is now back at Reddit).
The thing is, for any company that makes it big, there will be ambiguity over whether particular people are considered founders vs early employees vs key people post a merger or acquisition.
But for the sake of the origin story, the simplest is the best: two longtime friends wanted to start a company together, so they sought out Paul Graham, got into the first YC batch, started working on Reddit and got it to its early growth and success, then continued on-and-off running/directing the company even through to this day; it makes sense to call those guys the founders.
None of this detracts from Aaron's legacy. He achieved a huge amount in his life, and his time/role at Reddit seems minor compared to other things he did.
[1] https://www.reddit.com/r/reddit.com/comments/1octb/reddit_co...
[2] https://www.reddit.com/r/reddit.com/comments/1octb/reddit_co...