There is even more than pride here for Bayern to play for, when looking at the rest of the teams on Group A which one out of those teams seems like the one that could become more dangerous if they were to improve during the next weeks and months? And to me Manchester United takes that spot, so instead of just letting them remain on the competition and give them the chance to improve themselves and become a dangerous rival, why not eliminate them on the spot by beating them now that they are not playing well?
I think you have a point here and that totally makes sense. It is best to eliminate them now so that they won't ever have a chance to hurt you in the later stage of the game. Things like this has happened several times in football history and Bayern Munich knows this very well and won't let it happen. Just imagine they allow Manchester United qualify and United now beings in more players by January and becomes stronger and meet Bayern in finals and eventually win Bayern in the game. So Bayern will crush them totally now.
I slightly disagree as first of all Manchester United won't hurt more down the road than they do now and their game is at best on par with Galatasaray and Copenhagen, so it doesn't really matter who makes it into the next round.
Second, if Bayern gets the chance to do some rotation where needed, give some breaks or also give some of the players who didn't play as much some additional experience, that is probably ten times more valuable than thinking about an opponent they could be facing in a few rounds from now. Bayern will use that game for a lot of things, but they won't consider who will finish second behind them.