I think Daryl is taking one for the team by running off with Merle. He knows better than anybody that Merle will clash with everyone else in the prison. He sided with Merle so he could lead Merle away from there. Merle will big time Daryl eventually and Daryl will respond by putting a crossbow bolt through Merle's noggin.
"If I see another 45-year-old white woman from Williamsburg saying black lives matter, I'm going to punch you in the mouth." - Leslie Jones