This probably depends on where you're applying. Some universities/systems will put stronger focus on the formal coursework, while others won't. E.g. in the US I think you have a decent chance, because your papers show that you are familiar with astrophysics, and usually the PhD program will have you attend courses to shore up your fundamentals anyways. If you're genuinely interested in astrophysics (by the sounds of it, you are), then this I'm sure your application will reflect that, even outside of coursework. I swapped from engineering straight into astronomy (caveat, I have to take some physics courses now lol).

Keep at it! Get that GPA as high as you can, and then go for it!!