Your story is very similar to what ours. I went back to school (at night) when my son was 2. Every night, I would get home and he would be asleep with my husband in our bed. Prior to this he had always slept in a crib or his baby bed. Just before I started school, I got him a big bed and bought rails. This bed was not a problem. Husband would lay down with him in our bed. When I got home I was so tired and feeling guilty for not being there, I just slid into bed with them.
Long story short, my son will be 8 in May and has just now gotten to where he prefers to sleep in his own bed and doesn't end up in ours almost every single night. Up until a couple of months ago we would have a night here and there where he would stay in his bed all night. Mostly, he would go to bed in his room then come into ours at some point. We just have a queen bed, so you can imagine how crowded we have been as he has aged!
I went through a spell where I laid down with him. But, I ended up going to sleep too and would wake in the middle of the night, go to my own bed, and not be able to go back to sleep.
We have now discovered that he likes to have several of his stuffed animals surrounding him. I think this gives him the feeling of us being next to him. He loves to cuddle.
I haven't worried too much about his sleeping with us. I keep saying, he won't be 15 and still sleeping with us! I'll be lucky to get a hug then, better enjoy the closeness while I can.
I am not at all a fan of "cry it out", couldn't bear to do that to my child. We have done the "let him go to sleep on couch or our bed and move him" and "take him back to bed every time he comes to our bed". Neither worked for any length of time.
This is a new situation for him, he needs time to adjust to you not being there. That may be why he wakes up crying for you. It also sounds like he is a light sleeper. Get one of those "white noise" makers for his room. We have never done the "don't make a sound baby is sleeping" routine around our house. This seems to help them get used to sleeping sounder.
Since his bedroom is so far away from yours why not put a toddler bed in your bedroom for him to sleep in. I never thought much about it before children. But, I am SO GLAD now that our house is not designed with the master away from the other bedrooms. I would never sleep peacefully!
Good luck, it can be a battle with your child and with your feelings of guilt and tiredness.