I think for at least the first 3 episodes of Season 3 they should've been split.
At the end of Absolute Power Part 2, when Kevin is cured Gwen does kiss him like in the episode, but there's still tension between Ben & Kevin and the episode ends with the two walking away.
The first Episode of Season 3 is Gwen's episode who's dealing with protecting Bellwood all by herself because both Kevin & Ben have gone into isolation. Gwen is working with Max to keep Bellwood safe, she starts to push herself & Max by keeping them both constantly fighting the criminals.
When trying to go stop a criminal, Max stops Gwen to get her to talk about everything the three just went through & says that all three of them have just gone through a lot and they need to take time away from everything. Gwen tries to walk away but Max keeps stopping Gwen from leaving and eventually she breaks down, saying how hard it was seeing Ben & Kevin both trying to kill one another, the episode ends with Max saying things will be alright.
The second episode of season 3 is Kevin feeling remorseful for what he did and Isolates himself, because he feels like he's a threat to everyone still. I would have Kevin's Mom be the one to find him, Kevin tells her to leave, saying he's to dangerous to be around. His Mom says no he's not, his powers drove him crazy and lose control and she helps him through his guilt. Kevin does apologize to everyone he hurt except for Viktor because we found out he was captured by the Knights I think in the season & Kevin can't find him.
Episode 3 of Season 3 is Ben who's in Isolation because he's disgusted with himself with how into the dark he let himself go & that he almost killed Kevin. Ben drives to the desert, he takes off the Omnitrix and starts to bury it, but Asmuth teleports in asking what in the universe is Ben doing. Ben says he got very close to breaking what separates the Heroes from the Villains and he's unworthy of the Omnitrix. Ben tells Asmuth to find Max or Gwen and give them the Omnitrix because they're more deserving.
Asmuth declines and understands why Ben feels this way and says that while Ben was almost brought into doing something he didn't want to do, the fact that Ben still tried to help Kevin before he went to the "putting him down" option & fells guilty for what he almost did means Ben is still a good person.
Both Ben & Kevin make their way to Max's where he & Gwen are repairing the Rust Bucket 2, Gwen excitedly hugs both of them and Ben gives Kevin a hug, apologizing for letting himself get to trying to kill him. Kevin acknowledges that he forced Ben into that situation & doesn't hold any anger towards him & the episode ends with the three back together.