Please clarify my question, I am confused.
First of all, the risk of having such diseases is much reduced if a couple is having intercourse only with each other rather than with different people.
Secondly, It is Allah who has ordered us to get married in order to have intercourse. There is no questioning to Allah's orders. Most of the things that Allah has ordered have their answers in Quran and which answers are not available Allah simply isn't telling us rather than just to obey His command.
We come to this site to seek answers from either Quran or Hadiths. But if you question the ayats of Quran itself and there is no use..