Just because Jim was on Tarsus IV doesn't mean his parents were. Could be any number of reasons. He could be visiting other relatives, or (as that original script suggests) be involved in Starfleet training.
Indeed, since prime-George lived long enough to see Jim receive command of the Enterprise
, then logically speaking at least HE had to survive Tarsus (whether as a survivor of the massacre or not being there in the first place)
Also, we don't know that Winona was ever in Starfleet. The line in ST XI about her being "off planet" could also mean anything. She could be in the diplomatic corps, or involved in other such civilian work that might take her away from Earth. Sure, she was on the Kelvin
, but we don't know what she was doing there either.