Because that would mean admitting that it does harm, even if only implicitly, and that will cause a massive lost of trust from the public. Would you listen to someone who said, "Oh yeah, oops, I was totally wrong before, but now,
this time, I swear we got it right?" They have no choice but to hold to the party line, and hope that the numbers (i.e. incidence of autoimmune disease) stop rising soon. My personal guess, however, is that the numbers won't stop rising for a long while to go yet. They could have done it right early on and retained the majority of participants in the program, but now they've shot themselves in the foot.
Because look, everything else aside, it's not long before they admit that autism is an autoimmune disease. Kids with autoimmune disease should not get vaccinated, that's a given from both sides. Except the most "current" data (which is to say, medical surveys which are about 8 years behind the curve due to the time it takes to first diagnose a cohort of children born in a certain year, and then collect and analyze that data) says that 1 in 36 boys has autism. That's almost 3% of the male population right there, and herd immunity for measles requires
83-94% of the population be vaccinated. Nevermind the percentage of the population that has celiac (another 1% diagnosed, suspected anywhere from 3-10% undiagnosed,) rheumatoid arthritis (another .6%,) etc. Soon it will get to the point--if it hasn't already--that it won't matter what did or didn't cause it, the number of children who can't get vaccinated will make herd immunity impossible anyway.