Unfortunately in this case this is not possible, because there is no filter or action available on that part of the code. I would have definitely suggested a filter to use in the functions.php file, if that would have been possible 🙂
In this case just make sure to have a back-up of the header.php file so you can restore it, in case of an update. All the other custom CSS code will remain, but that file will most likely change in case of theme update.