This expression doesn't only mean stop, it can also mean slow down (just like you can use brakes in a car to stop or to slow down).
You provided a link to a dictionary that only mentions stopping – and I've upvoted your question for showing your research. However, it's often good to check more than one dictionary, as sometimes a dictionary won't quite capture all the possible usages of a word.
In this case, we can find more at Cambridge, which says:
put the brakes on to slow down or stop an activity : The city has put the brakes on further spending.
or at Collins, which says:
brake (noun) You can use brake in a number of expressions to indicate that something has slowed down or stopped : Illness had put a brake on his progress.
The expressions hit the breaks and put the brakes on are pretty much interchangeable when it comes to these metaphorical usages.