Actually according to authentic sources she was six years old at the time of their marriage, and nine years old at the time of consummation. The marriage, that was done with her father's consent, would best be compared to a betrothal or engagement in how marriage used to take place before moral decay here in the West. The marriage was consummated in the physically intimate way as posed in the question with a nine year old who was physically a woman, having reached the age of puberty as many young women do at age ten or earlier. Islam does not condone or support intimate relations with children.
In Islam, puberty is the stage of adulthood. That is when religious rites and duties are obligated upon men and women. It is also the time when it is known that a person is physically capable of reproducing. Unfortunately many societies treat young men and women who have reached this natural milestone as children until they reach an age that has been specified by man, which can change with the whims of the people. The result is a large number of young adults who are taught that they have no adult responsibilities until they are well into their physical and natural adulthood.