In his Red Rubber, Edmund Dene Morel makes clear on page 53 (of the later 1920 edition) that Roger Casement, then his informant as HM Consul at Boma, conveyed that "Of the fact of this mutilation and the causes inducing it there can be no shadow of doubt. It was not a native custom prior to the coming of the white man; it was not the outcome of the primitive instincts of savages in their fights between village and village; it was the deliberate act of the soldiers of a European administration, and these men themselves never made any concealment that in committing these acts they were but obeying the positive orders of their superiors." That said, the specific horrors of mutilation and its terroristic component may have drawn some precedent from punishments meted out by the slave raiders who attended Hamid al-Murjabi (Tippu Tip) in the East, and the chilling effect of same, but it's impossible to know--I've seen no smoking gun that proves it. If so that would be doubly ironic, because Leopold's regime was supposed to suppress those parties' activities.

As to the counterproductive sense, you may be laboring under the belief that the worker was usually the one punished directly with the severing of limbs. This was not the case. To compel the quota of rubber, a common feature was hostage-taking. Beyond the mistreatment in general of these people while caged (especially women and girls, who were subject to sexual violence that European informants can't even bring themselves to discuss specifically) failure to meet the quota would result in the hostages' mutilation. One of the most haunting images of the entire campaign against Leopold involves a father named Nsala, sent his murdered daughter's hand and foot as a reminder, after murdering his family as a warning for his defiance. So some of this was also rank cruelty meant to reinforce terror. I'm not sure if the cannibalism claims are true, but that's also a terror tactic.

When working-age men were mutilated, it was often in reprisal for their flight or their resistance, again as a message to others to render their service--although occasionally it was simply violence to instill terror across a wider region. To rein in independent acts of predation by soldiery, soldiers were supposed to return the severed hands or genitals of cadavers ("to prove they had killed men" as Peter Bate's documentary Congo: White King Red Rubber Black Death from 2004 notes, but also to account for the ammunition they reported having expended). e: This means that the African soldiers of the ABIR (the Force Publique) were also potentially subject to death or discharge (and possibly mutilation?) for failing to bring these trophies to the small corps of European commanders who were fearful of any sign of defiance and so also demanded these kinds of acts to prove that reprisals and punishments against those who resisted company demands were carried out. What's worse, those who were especially efficient reportedly received bonuses based on the number of hands or other body parts (smoked for preservation) which encouraged the mutilation of the living and the dead both.

So really, this was either punishment for those who were truly defiant or sought to escape (as a message to others not to resist) or punishment by the mutilation and murder of related women and children to send a message to the men to work harder and produce more--not to force men who were still actively producing to work with one hand or foot. It's as horrible as it sounds, because it rendered the entire Free State--an area so recently crushed by invasive slave trading and unable to mount strong defensive campaigns against Leopold's agents--more like a prison camp.