It's rather obvious why her Mum is packing her off to a clinic asap; let's face it, she'll be the one to take on a huge amount of the burden if her 16 yr old daughter has a baby.
I know a case like this and the young couple didn't manage to stay together for the length of the pregnancy. The boy was then going to the school formal with another girl, and on one occasion I walked past him in the main town library "chilling" and laughing on a sofa with another girl on his lap.
I worked in the same place as his mother, she and her husband tried their utmost to contribute and keep civil terms with the girl and her family, but it was an ongoing battle.
A battle mostly created by their son and his behaviour.
Maybe op's son wouldn't be as cavalier and irresponsible, but as the girl's mother; you can totally understand why you wouldn't want to end up with a grand child from your 16 yr old, living at home daughter, whose relationship with the baby's father may not actually last 5 mins.
Anyway op, no offence but your son is a dickhead for telling you he was using condoms and not using them. Unless they are saying one broke, in which case why didn't they get the MAP.
He's lucky he's not caught for 18 yrs of child maintenance and pressure to be a father to a child, hope he learns from it.