I hope this helps answer a few of your questions. Express Jet is Continental Express, as you know. It is less an issue of not getting along as getting along too well, between managements. Taking too many pilots from Express will cost a lot in training and slow down growth opportunities. Only so many can be hired and trained in a year. This is a common problem for pilots wanting to go to a certain airline. It happened to many pilots back when United was hiring a lot. It was more difficult, not impossible to get an interview if you came from Express. That being said, if you have very good connections, and can land an interview, it should not hurt your chances of getting hired. Generally it is harder to get the interview, but not harder to pass the interview if you come from the Express.
I assume your strong desire to work for CO is that you have relatives or family there. So, perhaps that would help you get in quicker. However, you could slow your career down considerably by tieing your dreams to one airline. I know guys that are flying as widebody captains in there early 30s because they took opportunities as they arose. You are probably pretty young and therefore will not have too much concern with the starting conditions at CO. That is a big advantage to you as many, myself included, could not afford the first year conditions offered at CO, but that is not what this thread is about.
You mentioned it in your post, so you are probably concerned about your decision to get an online degree. IMHO, that is not a good choice. Many friends have missed opportunities in their career because they chose to do what you are considering. In the regional world, you will not have time to study for school, work, have a family, and study for work. I would strongly recommend you to complete your education then pursue your career. As far as accepting or frowning upon an online degree, it depends. If it comes up, it will probably be frowned upon. Old grey haired captains that do interviews at major airlines, will probably not be as impressed as if you went the traditional route and got excellent grades. Usually, it will never even come up though in an interview. Very little time and if the box is checked they will just move on. I would not put on your resume XYZ "Online" University.
Well, good luck to you. Only you can decide what's best for you.
Cheers,
BBB