You'll have to head back up the way you came. It should be pretty quiet up until you get back to the subway. Unfortunately, it seems it's actually easier to get rid of the guards than to sneak by them. When you come through the door into the subway you want to get on the gargoyle to the left (so you're over the tracks). Eventually the guard with the jammer pack will come by near you and you can drop down and take him out. Do so and return to the rafters. move around a little so they don't find you.
This is not an easy area to clear. They have the infrared goggles so be careful where you stay but as long as you make good use of your baterang (don't use it too often or they'll find you) and take downs, it shouldn't be too much of an issue. Just remember to move around a lot if they find you. When you manage to clear this area, head out through the Southwest. When you go through the shutter door, you'll actually find a new enemy. This one has a shield. To defeat them, just stun them and hit evade twice. This will knock them down and they will lose their shield, making them normal enemies again. Be aware that their attacks can't be countered in any way so you need to just avoid them or take down their shields.
Keep going until you get back the subway terminal. You'll have to crawl through a vent to get into the room and you'll have a very large group of enemies above you. This is a tough fight. You'll have a couple of shielded enemies and plenty of people with bats and pipes. You should also watch for some thrown weapons. Use the takedown on the armored guy to save you some trouble. Then try and find and take down the shielded enemies. Even though someone else will pick up the shield eventually, they can put a real stop to your flow so keep the shields out of the fight as best as you can. Then deal with the little guys until someone else picks up a shield and deal with him. When in doubt, just evade until you have some distance.
