Having read many Smurf-related articles, I've never come through anything official regarding this. Source?
Although it's possible (and likely) he didn't like what his creation eventually became when the animated series showed up. A lot of the season 1 episodes were based on his comics and were severely altered, making them poor versions of the originals. Not to mention, several characters created for the cartoon were placed in the comics, probably against his will.
But there's no reason to believe he always disliked his characters, the early comics which were done almost entirely by him were great, not something you'd get from someone who hates the stuff he works on.
Although it should be noted that after Peyo's death, his state was inherited by his son Thierry, who pretty much has to approve everything done with the Smurfs. I have to wonder if he knew the direction this movie was going to take when he approved of this project.