Aside from The Robin Hood Society, The Twelve Army also has a personal grudge against the Bloodroot Clan because they are taking some of their clients. Although the Twelve Army is a very reputable company that provides private army services, they do not indulge or initiate a war against another business or group that their client has a grudge against. Their main purpose is defensive and not offensive which the Bloodroot Clan is doing.
That is why some of the businesses, groups, or personalities especially those in the underground sector would still hire a group from the Bloodroot Clan to inflict harm on others which the Twelve Army will never do.
Initially, Jacob just let this group do their way as long as they never go against the Twelve Army. Although he wants to have his way with them, that is just not practical and a waste of resources.