A.,
Everything we do as a parent is creating a habit. We feed a certain way, give bottle, have a bedtime routine... all habits. None of them are bad unless they physically harm the child ! So you have done things that are comfortable and have created a great bond and trust between you and your son. I would NEVER call that bad !
The question then is how to modify the habit if it no longer fits your lifestyle or age. Soooo.... It's like any habit, it will take time to change and patience on your part. I don't believe in cry it out because you can't really know if something is physically wrong with your child as was mine. I tried crying it out for almost two weeks and kept going back to the Doctor and he kept saying just keep it up. Ended up he had an intestinal infection and I didn't realize because I went against my motherly instinct to soothe him.
Anyway, you can create a new habit by gradually modifying your bedtime routine. It may be something that will take a few weeks or a few months. My children took a few months each. Just remember, in the grand scheme of things a few months isn't anything. Before you know it they will be 9 yrs old and you wonder where the time went ! (My son's b-day is today.) LOL
Send me a message if you want to talk. I have some ideas, but in the long run you have to do what is right for you.
Blessings.
M.