Creative-wise, Brock's leave was much more damaging, they had all sorts of plans for him and the show (SD in particular) wasn't as organized in 2004 as it was in 03..
However it wasn't just Brock who left, by the end of WM20 there was a mass exodus of the top names in wrestling for the 6 years previous (Goldberg, Rock, Austin, Hogan.. etc)
With Brock leaving they were struggling to find the next guy for his spot, it wasn't until a year later that they were going for Batista (and subsequently Cena, who really took that spot) as the #1 guy, but after so many ventures that fell flat on it's faces (JBL, Benoit, etc..)
With Punk there was much more emotional attachment from the fans, however business and creative-wise they were safe. They just went with the next over guy, and they did with Bryan (he was getting louder reactions than Punk by 2013), plus they had the Shield trio propped up and on their way, Cena was still on the show regularly.. it was no hair off their ass.
Punk, as pushed to the moon as he was, was not the big picture in 2011-2013, Rock/Cena was. He could've played a much bigger role in 2014 now that the Rock/Cena feud was over and he made his bones since the summer of 2011, but he decided to walk out.
Punk was bigger. He had his name chanted at shows for next 7 years.
Brock most people viewed as over pushed in 2002-04 and he didn't draw any money during that period whereas Punk had been #1 merch seller and year previous drawing on ppv with Ryback, Cena, Rock etc
He was not bigger, more over/more loved is the correct term. Brock crossed over as a star, his first UFC PPV bout drew 650K, in contrast to Punk's 450K. Keep in mind that was Brock's second lowest number in the UFC, while it was Punk's highest, taking in the fact that Brock was the sole main event of that event while Punk had Stippe/Overreem and Werdum/Browne as the two main events preceding him.
Brock's following PPVs drew consistently 1 million PPV buys while Punk's second and last drew an abysmal 250K.
Also worth a mention, taped Smackdown in 2003 with Brock as champion drew as much ratings - if not more - than live Raws in 2011-2012 with Punk as champion
People followed Brock in his ventures outside of wrestling, he had more name recognition with the casual audience that tune into wrestling every once in a while. Punk didn't have that reach, he had a cult following that adored and believed in him unlike Brock, but was never the star Brock was.