All of the copper bearing rocks we may cut can be toxic if precautions are not taken. First and foremost, NEVER cut copper bearing minerals dry unless you have a respirator on. I also would not cut them inside dry where all that dust can fly around and settle on everything. When we cut this stuff, we use masks and we have a fan pulling air out of the window that is right next to our cutting area. We also have a small fan running that blows toward the window ventilation fan to get as much of the dust out as possible.
From the research I've done on malachite, it appears that pure malachite does not contain arsenic. However, arsenic is found in and near other copper bearing materials, including malachite, and I would not rule out that some malachite contains impurities, which could include arsenic.
As always, it's better to be safe than sorry!