It's obviously unfortunate when these incidents occur in a friendly tournament. Clearly none of the players are expecting specific rules to cover this but are just looking for a 'common sense' ruling. With hindsight I can see that offering advice immediately was wrong and it would have more realistic to tell the teams that this would be looked at and a ruling published later.
So please ignore what I said at the time!
Firstly, I do think it is wrong to consider the score on the board when making the decision. That is incidental to the ruling and should not be a factor.
With a bit more time to think, I believe it is wrong to permit a substitute to play a board that has started. For example, the substitute may have been kibitzing the table, or another one playing the same hands. My approach would be to say that no result is possible on the board and award A+ (+3 IMPs) to the non-offending side (Laws 12A1, 86A). The hand should be played out only to get to the next one.
Of course my view is contrary to the practice in most tournaments on BBO, but there are practical considerations there that would make this approach less appealing.
Good luck!
Paul