Nope, it isn't apples and oranges at all. They two are completely related.
His veto did not ban embryonic stem cell research, but rather maintained his restrictions on federal funding of such. This action by the FDA deals not with federal funding, nor with newly approving a drug but with the level of doctor prescription required for an already legal drug. If the FDA runs every such decision by the president, then that would be micromanagement nearly on the same ridiculous level as Jimmy Carter overseeing the schedules of the White House tennis courts. The knee-jerk reaction to this decision, and hyperbolizing it as "Bush abandons social conservatives", is unbecoming.