If you're not trimming the visible fat from your beef before cubing or mincing or whatever you do, you'll need to do that. You probably already are.
It seems to me that you've got two things going on. First, you're trying to get too much mileage from your bacon and bacon fat. "Streaky" bacon is inherently greasy, especially the fat.
Starting with the fat, I suggest pouring it off completely after you brown the meat, and using the minimum amount of light oil (like corn oil, e.g.) to sweat the aromatics. You'll get plenty of bacon flavor from the fond on the bottom of the pan and from the surface of the meat without infusing the aromatics with grease.
Even if you've rendered it well at the beginning, hold off on adding the bacon until near the end of the process.
Second, you're moving the grease around too much to ever do a good job of removing. You'll need to let the pot settle down after the tomatoes have broken down enough to stay submerged, but while the "gravy" is still thin enough to allow the fat to float up and stay on the surface. That means getting the temp well under a boil and keeping your spoon out of the pot for 20 minutes or so.
By the way, there are a lot of right ways to make chili, and this isn't a criticism of Phatch's method.
I prefer to thicken at the end with a masa and/or flour/water slurry, rather than thickening at the beginning with a roux. In your case waiting to thicken will allow you to degrease. As you near the end of the process, reduce the heat so the pot doesn't bubble at all and stop stirring. After 20 minutes or so, the fat will rise to the top and you can skim it. Then increase the heat to a slow boil (you'll need to see actual bubbles or the flour won't fully homogenize and cook), add your slurry, stir until the mixture thickens, and adjust for thickness by adding more slurry if necessary. When you've achieved the desired body, return the bacon to the pot, and simmer for at least a few minutes more to allow the flavors to marry and the consistency to fully stabilize.
Chili is so individualized it's hard to come up with a universal set of rules. Here, I'm sticking with cooking basics rather than chili specifics.
Hope this helps,