Kennedy had slashed the number of recommended vaccines from 17 to 11, sparking a backlash from health experts.
The US retailer's announcement follows commitments from several food companies to phase out artificial dyes.
Casey Means was questioned in a confirmation hearing on everything from her stance on the flu shot to her lack of an active medical licence.
Health experts fear a future where measles outbreaks keep taking over towns with low vaccination rates.
State health officials say over 500 people and students in 15 schools are in quarantine after being exposed to the measles.
The changes receive mixed reviews from experts, in particular over concerns some could lead to people eating more saturated fats.
The overhaul is the latest in a host of sweeping changes made by the Trump administration.
Trump, who called the decision "very good", has directed the health department to look into making more changes to childhood vaccinations.
US health secretary Robert F Kennedy Jr has questioned the safety of the vaccine and downplayed the risk of contracting the virus.
