I think you have done great to get him to sleep in his own bed and I can understand your concern that if you let him come in and nurse and cuddle with you early in the morning especially when you used to have his daddy there and no longer do that this might set up a very bad habit which will be hard to break.
From his standpoint, he may be sad or scared or lonely and want reassurance that he is not alone and abandoned in the dark of night. One year olds cant really relate to time and when it is appropriate to be awake and noisy and get others to respond. I think that in the long run when children get what they need when they need it that they grow out of it more quickly than if they get more and more upset and don't understand why no one cares how they feel at certain times of day or night.
You are probably more tense and feeling the weight of responsibility right now with two little ones you are with day and night with no one to take over and share the tasks and responsibilities. When in doubt, it is always best to do the most loving thing...
Good luck to you in this very difficult time. (It isn't a battle which you will be giving in to...you might both win in the long term)