I found it! It took "only" 2 years.
I used Keyboard Layout Manager (unfortunately the website is down). After installing (run as admin!) click New, select new name, your language and your current layout as template. Then just change , on numpad to . and confirm with Ok.
In my case I removed the old layout from keyboards list, so only the new one remained. After this, the language bar dissappeared. But after logout/login it reappeared again and... everything worked as expected! Yay!
Also, no DLL for your new layout is generated so it only works locally on any given computer, it's not a portable solution. There is also a registration fee for this software, but a freeware version can handle dot/comma substitution.