OK - now answer this - why do they let Thawne go?
Because the deal was he tells Barry how to save his mother, they let him go.
OK but why stick to that deal? They have been running an illegal gitmo-style prison all season, breaking the deal with a sociopath is small fry - why would you let a sociopath who previously traveled in time to kill family members, has killed many more people leave with a time machine.