If you haven't quite gotten this trophy by the time you complete the game, never fear, there is an easy way to do it.
Use Chapter Select to load up Chapter 2, then make you way through the sewers and the mechanical room area. Make you way through the first courtyard area as well, where you will be able to get a few stealth attacks in. Soon you will come to a large gate where you first have to climb up and disable the alarm, and then you and Flynn will lift the gate together. This is where you want to be.
There are six guards in this area, and it is pretty easy to take all of them out with stealth attacks. But just get as many as you can easily do, then pause and Reload Checkpoint. You'll be right back at the beginning of this room andyou can take them out all over again.
Rinse and repeat until you get your 50 stealth attacks and your trophy.
Note: The trophy will unlock right away as soon as you get number 50.