Why did Sebastian Moran shoot the businessman Alfred Meinhard?

The confusion increases if we go by the scene staged previously where Sebastian Moran is smoking his Tekel blend cigarette at the entrance of the opera, ready with his equipment concealed. As he sees Holmes enter the opera he gets up and leaves for the rooftop of the building opposite Du Tromphe Hotel to prepare his sniper.

Now the question is : if he saw Holmes acting according to plan why bother to shoot the man as the bomb goes off? Correct?

If you observe clearly, he took the shot seconds before the explosion occurred. We mustn't forget that he was the best marksman in the British Army. So when he saw Meinhard was about to send the bomb off - He pulled the trigger. He couldn't pull the trigger too early as then Meinhard would collapse and leave the casket unopened. Too late, and the body would be blown off and it would no longer be possible to shoot him. Even if he pulled the trigger at the moment of the explosion the shockwaves would deflect the bullet.That is certain. So you see what an expert he is.

I think the director wanted to highlight the dialogue leitmotif in the movie "No loose ends". I am saying this because he cunningly makes the character of Claude Ravache speak the same words moments before. Ravache probably managed to make the explosions happen by being influenced by the meticulous nature of Moriarty's skills. Hence, he remained faithful to his plan of suicide even as Holmes offered to help him. I think it is this nature of Moriarty that wooed a person like Moran to take his calibre to the next level.

Moran acted accordingly as per the plan. He didn't want to leave loose ends in case the bomb blast left Meinhard injured and he lived to deduce that Moriarty was behind all this.

I am surprised you didn't take note of it in two moments in the film. The first was the assassination of Dr. Hoffmanstahl even thought he was destined to die by bomb blast. The second was the murder of Rene as he failed to kill the German Minister. So you see Guy Ritchie has employed intricate devices to glorify Moriarty as the supervillian. Hope this helps.

It was a back-up plan. As explained on the Wikia:

In 1891, Meinhard traveled to Paris to attend a business conference at the Hôtel du Triomphe. Unbeknownst to him, his movements were being watched by agents of Professor James Moriarty, who had secretly been buying up all stakes in his company with the intention of taking it over. However, in order to complete his takeover he needed to take Meinhard out of the picture.

Moriarty arranged for the Sept Grenouilles bakery, which served as the hideout of anarchist Claude Ravache, to be contracted to bake the cake for Meinhard's conference dinner. He then had Ravache plant a bomb in the cake, knowing that it would be seen as a revenge attack for the bombing in Straßburg (which Moriarty had also orchestrated).

In reality, the cake was only a distraction for Sherlock Holmes, who Moriarty knew was tracking his movements. As a backup, Moriarty had his henchman Colonel Sebastian Moran, an excellent sharpshooter, stationed on the roof opposite the hotel. That way, in case Holmes managed to find the bomb in time, Meinhard would still die.