This discussion may contain spoilers!
I am surprised that no one has yet to mention something that clearly explains why Luke had every reason to not be with the group at the end. No, it's not Kenny or even Carver for that matter, but Carlos.
Remember when Carlos pulled Luke aside to have a private talk? You would think it was to talk about Nick shooting Matt, but that doesn't seem like something which had to be private. Since they are also the biggest forces of the group, it would be foolish to think they did not set up a secret plan. My guess is that Carlos was aware that the group was still being followed, or perhaps he just wasn't convinced and wanted to devise a plan just in case.
One thing for sure, it seems that Clem is needed by Luke. He knows she is young but also very smart. She survived on her own, managed to escape a locked shed, escaped walkers alone, had Carver leave the house, protecting Sarah in the process, and she can do things others can't.
Carlos has Sarah to watch over. She has some mental problems and he knows he is the best to take care of her because he is not only the doctor but also her father. Rebecca will give birth in episode 3 (confirmed by the episode 3 background image) so she is pretty much useless. Alvin, the husband, wants to keep both Rebecca and the baby safe. Being fat doesn't help his case either. Nick, distraught and emotional, is clearly not a good helper, this being evident when he shot and killed Matt. This leaves only Clem to help Luke without concern.
Now while this sounds extremely vague, you need to realize that Carlos was confident that everything will be fine. Either he knew something that no one else knew (something that he told Luke), or he didn't believe Carver would kill a doctor. The fact that Carver didn't slit Carlos's throat and the fact he didn't shoot Carlos but instead targeted Walter, Alvin, and Sarita/Clem (depending if you surrendered or went to look for help) confirms that Carver only intended to kill people he didn't know or people he hates. Alvin is an example, who killed a member of his group (he will say this if you surrendered) and being the husband of Rebecca, which is definitely a concern to Carver who is convinced she is carrying his baby.
And regarding Luke's whereabouts? He most definitely left to Carver's camp. He obviously knows where it is as he was there before so I bet he already went there to find a way to get them back out. He could also be looking for people willing to overthrow Carver, such as the group in the episode 4 background image. Notice that Clem puts blood on her face as if she is ready for war, and doesn't Luke look like one of the silhouettes?
Any thoughts on this? Seems pretty evident if you ask me.