If it's stressing your cats out AND if your sick cat is already on antibiotics, I'd go ahead and let them stay together. Deagan's already sneezed and breathed all over Murfie anyway. If Murfie's not showing any signs of being sick, then they're probably fine together. However, you might find that Murfie is sick with the same type of upper respiratory junk in about 2 weeks. It doesn't mean that Murfie has herpes, just that he's caught the viral infection.
The herpes virus lives in the lining of the brain and is triggered mostly by stress, but other things can trigger it as well. Cats that have weak immune systems are most susceptible to catching the herpes virus, although it can be passed to a kitty from its mom. Because herpes weakens your cat's immune system, any time your cat gets sick from any kind of infection, it will take your cat longer to get better. Strengthening your kitty's immune system by providing a good diet is one of the best things you can do to help your kitty stay flare-up free. Also keeping your home as stress-free as possible will help, too.
Lysine is excellent because it interferes with the virus' ability to reproduce during a flare up. When my cat is having a flare up or dealing with some other type of problem (like a bacterial infection right now), I give her 1000mg a day. I buy the NOW brand powdered stuff and give it to her in her wet food. I give her 500mg/2x day. The effects of lysine only last about 8 hours or so, which is why I do twice a day. I started off buying the 500mg L-Lysine tablets at Wal-Mart and crushing them and adding to her food, but that got old real quick, so I switched to the powder. When she's not having any symptoms, I give her 500 mg a day (250mg morning and 250 night). It takes a good month of daily doses to see any positive benefits from the Lysine.