I'm in the same situation, and I have submitted the application package. In my case I'm sponsoring my mom, she's separated from my dad for 15 years. I included an explanation letter saying that my mom's marital status is legally separated because we followed ircc guide definition that legally separated is a person that is married but is no longer living with the spouse. And that it should be enough reason to not consider my dad as a dependant. This was also what the cic agent advised me. With it also included is the affidavit of separation from my dad and mom as well. Both notarized. My mom's statement says that she promise she will not sponsor my dad at anytime in the future. And my dad's statement says that he has his own family now and he does not wish to undergo the medical examination..
It's good to include proof that divorce have already been filed. It will make your case strong. For my parents they cannot file it because there's no divorce in the country where they got married, annulment costs so much money and they cannot afford it so it's not an option.