I dislike him much more for Prometheus and the ending of WWZ. I don't think I've ever hated a movie as much as I hate Prometheus.
Well I loved Prometheus, but the "problems" with the film came from Ridley Scott as he directed what Lindelof was to write. Scott had a very specific vision for Prometheus and gave instructions to Lindelof on what he did and didn't want answered. In interviews, Scott himself has confirmed this and said the end product's success or failure should really be on him.
To hold any one person responsible for WWZ is a mistake. The making of that film is an incredible story in how a script can get thrown around so much as to be unrecognizable to the original writer (JMS). Lindelof was brought in after much of the movie had already been filmed and people were realizing it wasn't working at all.