I like both pairings to be honest, and I hope that both work out. Hell, I even hope he gets it on with Kaguya too.
Kallen/Lelouch is a different relationship from C.C./Lelouch. C.C./Lelouch is a relationship that originally grew out of necessity, she being the one who gave him his Geass, and the only one he could expect answers or information from. Lelouch/C.C. was played up big time during the first season because C.C. was the only one privy to what is really going on. She was the only one who truly knew Lelouch, and everyone else was meant to view him through the persona of Zero. She was really all he had, and they grew fond of each other over time due to their necessary close association. However their relationship didn't take off because each of them realized what was truly going on, they were just using one another, and they still are.
Kallen/Lelouch was sparked by Kallen finding out who Lelouch really was. Now she was in on the secret and enjoyed a level of closeness to Lelouch almost on par with C.C.. Coupling that with her previous hero-worship and interest in him from school, the outcome is predictable. Kallen/Lelouch has no "we're just using each other barrier," Kallen genuinely believes in Lelouch, and after Lelouch came out of emo mode with the "power of friendship" he is less willing to view his own men as pawns to be sacrificed, especially Kallen. Kallen/Lelouch is more of a relationship motivated by actual feeling rather than fondness born of necessary association. This is why Kallen/Lelouch progresses a lot quicker then C.C./Lelouch.
When C.C. is next put in danger, as has been forshadowed, Lelouch’s relationship with her will grow, and his relationship between both Kallen and C.C. are not mutually exclusive.