What is the best way to thicken the liquid in this recipe?
If you are making a tortilla filler then you probably don't want that much sauce in the end product, so rather than thickening it you might want to consider reducing the amount of liquid that goes into it in the first place. Peppers and onions both shed water as they are cooked, and canned tomatoes have water as well. You don't want to lose your peppers, so I would suggest adding less canned tomato and substituting it with some tomato paste. How much to do depends on the quality of the canned tomatoes, as there's a big difference in quality out there. You get what you pay for - cheap canned tomatoes have water added to the end product, you'll typically get a thicker result and richer flavor with good canned tomatoes as there's more tomato in the can in the first place. That may be all you need to do. 

My go-to thickeners are roux, cornstarch and arrowroot powder. A roux is flour fried with butter which is then added to the dish and cooked to a temperature that activates the thickening properties. The good thing about roux is that you can cook it to different levels to add flavor to a dish, but in this case you don't probably don't want that flavor. Cornstarch is relatively flavorless and needs to be heated to a certain temperature to activate it's thickening properties. Arrowroot is a plant product that thickens at a very low temperature, so you can add it after cooking to warm food and it will thicken it without more cooking. In fact, cooking it too much will break down it's thickening properties. It thickens almost instantly too, so there's less guesswork, you just add and stir until it thickens to the consistency you want. Both cornstarch and arrowroot should be mixed with a small amount of water into a slurry before being added, adding directly in powdered form tends to cause clumping. 

Another option would be to add a small amount of gelatine at the end of the cooking process, this would thicken up the sauce when it gets cool, and has nice mouth feel. 

So first you could try adding a bit of tomato paste and less tomatoes, or using a thicker brand of canned tomato. Or you could thicken using cornstarch or arrowroot depending on whether you plan to cook the sauce additionally afterwards. Experimenting with gelatine might be more work than you want to do, but it has nice properties.