A good deal of it very well-deserved. For a movie exposing the blind-alley of rampant consumerism, it was being sold via a dizzying array of Cheap Plastic Crap, much of it bundled with the very junk food the movie skewered.
Even coming from Disney in the first place the message came across as the old argument of a priest-of-past-sins being preferable to a priest-of-purity.
Are you saying that the employees that make up Pixar are, on the whole, frequent and regular customers of the fast food industry?
I would expect that living in/near the bay area would give them good odds of being in a different demographic.
Intentionally try to send a message to a demographic by placing Wall-E in their natural path would be a decision made by the corporation well above the level of Pixar's animators. That body would almost certainly be the same one that green-lit the avalanche of Cheap Plastic Crap.
So, even if they believed Pixar's message, and were intentionally trying to preach to those at-risk, they were saying "you should learn from Wall-E" (do as I say) while simultaneously saying "also, buy this plastic crap" (not as I do).