I appreciate your candor in acknowledging you failed to follow WOA protocol and guidelines. Now, about the protest you suggested the coach would be a fool to file.... 
You indicated that "I never make the determination, I merely state that I am concerned, due to the player exhibiting one or more signs, and therefore am removing them from the game." But that is not what you did. You refused to allow the player to re-enter, which is what caught my attention (and apparently caught the coach's attention). In refusing to allow the player to re-enter the game, you necessarily had to make a medically related decision. You decided that the player was not medically "fit" to re-enter the game. Here are your exact words: "We said go right ahead, but your player is not stepping back on this field and we will be including the fact that you tried to sub back in a head injury." You "diagnosed" the player as having suffered a "head injury." My only point is that this is not your role.
You indicated that: "Having gained more experience, I will also let the coach sub the player back in, but I will also make sure to note that in my report." Perfect.
Word to the wise: given how litigious our society has become, you definitely do not want to take an action for which there is no insurance coverage. The $37.00 per game they pay (or whatever the salary is these days) is not worth the risk! Stick with the WOA's advice!
I am always trying to learn and do a better job with every game I work, every assessment I receive, and every training session I attend. And you are correct, given today's out of control litigation I should really be asking myself whether or not I should even be reffing. If a parent is willing to name me in a lawsuit because I denied re-entry to their child due to an apparent head injury, then it is just no longer worth it, period.
I think I am correct in assuming that you are not neccessarily having trouble with the "morality" of what I did, just the "legality", and my departure from official protocol? In the LOTG Law 5 The Referee - Powers and Duties - bullet-points 7 & 8 address injuries to players, in which we are given the "power" to judge whether or not an injury is serious or only "slight" in our opinion. We have also been told to treat any head injury as serious and therefore stop play immediatley. So I do think that assessing an injury is within our role, can I say that they have a concussion or make a medical diagnose of fact, no, can I say that they have suffered a serious injury (ie; head injury), yes - in my opinion. Was I, and the Ctr, correct to deny re-entry to the player, not according to the WOA advice, were we within our powers as referees, I believe so.
I think in the future, rather than just telling the coach that their player cannot re-enter the match, I will ask them if they really think that that is a good idea, seeing as how they left the field displaying symptoms of a concussion (as given to me in training by a medical professional). I personally think the WOA's advice is nothing more than CYA and a bit chickens__t, but they are the bureaucrats, not me.