You can’t stop it. There are just people who will want to get ahead of the game in any way possible, and Pokemon GO is not exempt from it. People have so far resorted to using bots, GPS spoofing, emulators, and other such ways just to boost their collection of Pidgeys and Rattatas, and Niantic is bearing down on these with permanent bans.
Niantic has specifically stated the reasons for permanent banning in one of their new pages (more on this in a bit) – “This includes but is not limited to: falsifying your location, using emulators, modified or unofficial software and/or accessing Pokemon GO clients or backends in an unauthorized manner including through the use of third party software.” That’s pretty substantive and goes across the range of Pokemon GO cheats out there.
Niantic has also quietly launched an appeal page, which means that at the very least, you can still make your case if Niantic decides to ban you from the game. There is a form you have to fill out, and banned players are invited to make their case for a second opinion. What is not so transparent is how lenient Niantic Labs will be, or what sort of turnaround time can be expected in this appeals process.
It’s good that Niantic is at least ready for the eventuality that a permanent ban handed out might be justice wrongly administered. But to those who use bots and emulators and stuff, they probably deserve what’s coming to them.