What I remember from when my older kids got eye-infections (conjunctivitis) and I caught it from them, (ewwww, don't let him put his hands near your eyes!) was that they weren't really "sick" either. But they did wake up completely in the night when they would have normally slept through because they were half waking up, like we all do, trying to open their eyes and they were stuck shut, which scared them. I kept a damp cloth by each of their beds to wash their eyes and then comforted them and tucked them back in and went and washed the cloths out, put clean ones back in case they woke up again, and went back to bed myself.

If he's already on medicine for it (do they still give antibiotics for conjunctivitis?) the discharge is probably already lessening and maybe you'll get lucky and he'll sleep through! If not, I'd bet that warming up his blankie and keeping him company for a few minutes will probably do the trick again.

Good luck!

Sometimes if my kids are sick and can't sleep I have taken them into bed with me or sit on the couch with them lying down the couch. I gently stroke them and they soon drop off. After they have been asleep for a while then I have moved them back to bed. You could try doing this on their bed if they are in a bed.

What you did sounds like a good idea too.