Should I focus on my grades or on finishing my degree on time? I am doing an 5-year Integrated Master's degree (3-year Bachelor + 2-year Master) on Physics in Europe. Aiming for a thesis in Quantum Computation/Information. I am currently on the 4th year and have a "good" overall grade (84%). 

However, due to health issues, I failed to perform well on my 6th semester (the last of the Bachelor), almost failing half of the courses. I got 50%-60% on 4 of them.


  So I am faced with a dilemma:
  
  
  Should I focus on finishing my degree on time, potentially having to either manage doing a thesis and improving some grades at the same time, or settle for those low grades and just move on?
  
  
  OR
  
  
  Should I focus on improving my grades and achieving the ones I know I am capable of, potentially getting to ~88%, with the
  disadvantage of having to delay/prolong my thesis to a 11th semester?
  


This might be a very close call and depend on a lot of factors, but I am interested in knowing, in general, which option gives me the highest chance of success in continuing my academic career with a PhD.

Not sure if a Postdoc would follow after, but I eventually want to go for a top-tier job in industry, either related or not to research (like IBM's or Google's Quantum Lab, or some other not focusing on research).
Usually there is a scheduled time and an expected number of credits for a degree. A BSc normally takes 4 years, with a given number of classes. This is because the ability to absorb the material in the allotted time is part of the evaluation of the student. 

Ordinarily that is. But you mention health issues.

If you had some major life altering illness then it is something you should discuss with the university. I mean something like as serious as pneumonia. I had pneumonia a couple years ago. If it had happened in university it would certainly have cost me a term, maybe a full year. 

Under such circumstances, and presuming you now have some kind of control of the situation, you should consider repeating either a term or a year, depending. 

First talk to your favorite prof or your department chair. Ask if there is the possibility of repeating the year. Or possibly repeating only some of the classes. In most cases, they will want to help you. It looks good for them for you to perform well in the university. They will nearly always want to help you finish the degree.

Be open to their suggestions. They may have suggestions of alternatives.