I think the answer is quite clear in one respect, that break of journey is not permitted if you are on the outward portion, but undoubtedly permitted if using the return portion. There are further arguments regarding the enforceability of this restriction which depends on a whole host of factors such as whether you were advised of this at the time of purchase but this is all a bit pointless in your case because you are certainly not going to get in trouble this time.
As to whether it is worth lodging a formal complaint regarding the incident. It really is up to you. From my perspective, if I were you, I wouldn't bother, as one I have far too many important things in my life worthy of my attention to worry about something like this, and two I seriously doubt that Northern's subcontractors are at all bothered about the reputation of their staff, as long as they prove to be cost effective for Northern. It is highly likely that this will just be brushed aside and an insincere apology issued, and even if an investigation is carried out, the guy will likely just deny it, and there is not very much that can be done unless his colleague backs up your story, the chance of which happening being slim to none. In my opinion it will just be a waste of time complaining about this incident.
On the other hand, this behaviour is clearly unacceptable, and if you complain, it may be recorded in that employee's file, so it could play a part in the future possibly in deciding whether disciplinary actions may be appropriate. Also if it really bothers you, then feel free to complain, and do whatever makes you feel better, because your own wellbeing is the most important thing to you.
Whichever option you choose, there is no right or wrong answer. Do what you are happiest with. In addition, you may have technically been in the wrong, but it is hardly something worthy of losing sleep over and you certainly shouldn't feel guilty about breaking your journey at Manchester.