After you reach the first yard, Trinity mercenaries should be standing in a way that allows for silent takedowns. Especially that at this stage into the game, you already own a knife. Sneak up to each soldier from behind. The key to cross this area is avoiding the alarm, but also quick and careful acting.
Do the same after you reach the corridor in the catacombs. Wait a moment for the soldier on the left to walk away and eliminate the two, one after another.
At some point, floor will collapse under you. There is no way to avoid the fall. You fall into the lower level of the catacombs.
After you take several turns, you run into a patrol of two soldiers. They will walk to the left side of the location, where they start looking at a hole. It is a perfect moment to use the bottle nearby. Take it, craft a molotov and throw it at the enemies, Then, cross the hole that they have been examining.
In the room where the mercenaries keep Sofia and the rest of the remnants, lean out and aim the bow at the soldier facing away from you. Select the poison arrow and shoot it; thanks to that all four opponents drop dead.