I'm curious as to why "the comics" make you think this, given that this exact version of Aqualad doesn't exist in the comics.
Regardless, this Aqualad "going rogue" would fly completely in the face of the entire theme of the first season, that being that you are not your parents or your genes, you are your own person.
I know some people think it's fun to speculate, but is it at all possible that there's just a touch of overreaction taking place based on very little material?
http://en.wikipedia.org/wiki/Aqualad_(Jackson_Hyde)
Ok, I was wrong about him being the son of Black Manta, but his criminal parentage is still there. The costume and the way in this series that he is the son of a henchman called Calvin Durham who worked for Black Manta just screams to me that he will return as an enemy. Also just watched the episode again and think I can account for the missing members of the team:
-At the end of the episode when the League and Young Justice come to see Tim Lagoon and Beetle, The Flash is standing in the background with Batman and Aquaman. The way he stands and considering this is a five year gap and he has done it in the comics, I think Kid Flash may be standing in as Flash for Barry for some reason. Could make sense since Dick did change his hero name.
-Artemis could have become Tigress and gotten together with Icicle Jr. It's a big change but there were plenty of big changes in this episode so I can see Artemis also becoming a villain and changing her name.
-Since Green Arrow and Black Canary were present at the end of the episode, I'm going to assume that Red Arrow had gone to travel on his own in search of Speedy. What happened I have no idea.
Things I can see happening in this season:
-Ra's al Ghul bringing Jason Todd back to life and him becoming the Red Hood
-Match trying to infiltrate the Young Justice team and several fights between him and Superboy
-Superboy and Wonder Girl together, while Miss Martian stays with Lagoon Boy. Then Superboy and Miss Martian start missing each other
-Love triangle between Nightwing Batgirl and Zatanna
-The whole 16 hours thing being revealed to have been an attack on an alien planet by the big six. Then this would spark war and the Light would have been supplying them with the necessary things to win the war.
Just general ideas I had, nothing serious.
EDIT:
http://www.youngjusticelegacy.com/
"One will rise"=Kid Flash becoming Flash
"One will fall"=Aqualad becoming a bad guy
"One will die"=Artemis is dead?
I think I might sign in to this website as it looks pretty interesting... Sounds like confirmation for the three original missing members...Poor Artemis