Young gun, you were confronted by a situation, that you rightfully concluded provided, intentionally or unintentionally, an unfair advantage to Team A, at Team B's disadvantage. You analyzed a number of possible alternatives and selected a reasonable solution. Sounds a lot like you complied with the exact purpose of NF: 1-1-6 (The referee has the authority to rule promptly, and in the spirit of good sportsmanship, on any situation not specifically covered in the rules......".
The Team A coach may have been unhappy, but that was because he was wrong, and although what he allowed may have seemed like a really great idea at the time, and may have been totally unintentional, it did place his opponent at a possible disadvantage, which you promptly and effectively eliminated.
You selected one of several possibilities, and the one causing the least consequence. That's your job, nice work.