So, just make that an option that your users can set in your app's Preferences. Of course, burdening the user with this decision is the easiest solution for the programmer. ;-) I'm sure I'd personally prefer to decide myself whether I want lists of numbers in German or English in my apps, even if the GUI is English. I see your point, but I still feel this is too much fuzz to expect the user to set this in each and every app that deals with numbers. For apps where numbers feature a most prominent role, maybe, but my app doesn't fall into this category. So I think the only acceptable solutions are either a consistent automatic setting (at least as default), which is what I tried to implement, or user-definable separate locale settings for various GUI languages in System Preferences, which is up to Apple.
So, just make that an option that your users can set in your app's Preferences.
I'm sure I'd personally prefer to decide myself whether I want lists of numbers in German or English in my apps, even if the GUI is English.