Unfair penalization of Bachelors thesis resulting in a "downgrade" of my degree
I think that your assessment that there is not much that you can do at the moment is correct. Your supervisor (and the other faculty member) should be the ones to address this issue at the faculty level. You should however check the University's regulations regarding the possibility of appealing grades and decisions about "summa cum laude" status. In particular, check if there are any deadlines for doing so. (If there is no tight deadline, you might want to give your supervisor some time to try to sort things out internally before filing any official appeals etc.)

As far as this issue affecting grad school applications. Again your assessment that you should not mention this in your application is probably accurate. Doing so may come off as "whiney" or you trying to avoid responsibility by blaming others. However, if your supervisor is providing a reference letter for your applications, it would be good if they could address the issue in their letter.