A violent way of rendering a planet uninhabitable being the obvious: accelerate a large enough object to a sufficient velocity that everything on the planet goes the way of the dinosaurs.
Put briefly, an alien race secretly constructed a series of autonomous spacecraft that would go to other solar systems and snuff out the inhabitants without them ever realizing they were under attack. The way that comes to mind, broadly speaking, is something relatively slow acting and environmentally based, such as inducing a star to start CME-ing the crap out of the planet (not that I really know how exactly you'd go about doing that) and strip its atmosphere. At the same time, it preferably shouldn't take a million years; you want it to be slow enough to be chalked up to some nasty natural phenomena, but quick enough to kill everything on the planet (or merely drive them out).
The tech level I'm working with is pretty darn advanced. While the alien weaponmakers can't use the power of handwavium to crush everything before them, if it's physically possible, they can (probably) find a way to do it.
tl;dr, what are some plausible ways to strip a planet of its ability to support life without the locals figuring out they were being targeted?
Edit: Changed title to subtle. D'oh. The comment pointing that out is right; killing things is violent regardless of whether or not you're shooting them or poisoning them. As for the tech level of the target planet, they're interplanetary, but an order of magnitude less advanced than their attackers. The aim is to destroy the sentient life only, but if that's too tricky, the aliens are more than willing to just kill everything. They'd just prefer not to.