I use the cry it out method, but when they are sick or teething, I see no problem with comforting them as you are. I use regular baby aspirin to help them stay asleep, for pain, but only when he seems really uncomfortable. I also found that letting him chew on pretzel sticks made him very happy. You might just have to tough this period out, and when the teeth come in, get him back into his bed. I would put him to bed in his crib each night, but if he wakes up and needs extra comfort, go ahead and give it to him, and that may, unfortunately, mean some sleepless nights for you. If dad is around, ask him to take his turn.
I hated cry it out initially, but after not sleeping for 18 months with my first child, found out that there is nothing wrong with letting them cry for a bit, so long as there is nothing wrong. (like pain from teething) The longer you let that go on, the harder it will be to get them to learn to sleep on their own. Experience talking. But, to each his own. It only takes one to three nights of using cry it out, they give up the crying pretty quickly once they figure out you are not going to respond. Then, when they do cry, you have a better sense when there is really something wrong, another benefit of cry it out. If you can't take it, try to spend time elsewhere in the house while your husband handles it, or go out. That is what worked for my cousin and his wife. Believe me, I understand, it is hard to let them cry, but sometimes it is for their own good.