I think something that's important to realize is that a lot of the players that use Siege Charge to loot are usually the first players to arrive at the area that they wish to loot at. For times that I wish to use Siege Charges to loot in the Treasure Room of the Cursed Caverns, I will change servers until I come across a location without anyone else already present. The issue and reason that I support grenades going through other players during PvE is that some players choose to join a looting area and stand in front of the grenade user who was already there, and disrupt the player(s) present.
In addition to looters running into these problems, the usefulness of grenades cannot be forgotten during invasions. Jolly Roger can be tough to fight against, especially at close range, leaving ranged weapons as the ideal choice. Grenades allow smaller groups of players to have a better chance, and letting grenades go through others during invasions can help enable more successful runs of invasions.