No one is alleging a conspiracy - not sure where are getting that from. Two of the three bike officers that originally arrested Gray are charged with assault and improper arrest. The third is also charged with man slaughter (not sure why his charge is different - maybe failure to secure Gray in the van). The basis is an illegal stop and no illegal knife as reported. Separately two additional officers who interacted with Gray/van are charged with manslaughter plus other charges for failing to aid Gray despite his request for help and being in obvious distress. The most significant charge was for the van driver who was charged with depraved indifference murder because he did not provide aid to Gray despite his obvious distress. Clearly there is a lot of additional facts to be determined at trial but your assertion that Gray's death is either a series of non criminal screw-ups or a conspiracy is nuts. The determination is whether those screw-ups by the individual actions of six officers are criminal. The prosecutor believes the officers actions were criminal and we will see what a jury thinks. A healthy man who committed no crime is dead when in the care and custody of police. (And btw, running from the police is not a crime but it can be probable cause. Since the charge reported by the bike officers was false, knife was not illegal, those officers were charged with assault and illegal arrest.)
Fleeing from a lawful police stop is a crime. I don't know exactly how the stop unfolded and that's why I said that I don't know if the running away was a crime.
The knife situation is interesting. Maryland has a relatively complicated set of laws around what knives are legal for open carry, concealed carry, or just illegal. I suspect the cops are going to argue that the knife was in fact illegal, or in the alternative, they are immune to prosecution. It's a problem to be prosecuting police for making arrests that the prosecutor later determines not to charge, unless the arrest was truly made in bad faith.