Hi there, most of the graduate school applications that I filled out had a section for outlining any extenuating circumstances during your undergrad that you would like the admissions committee to take into consideration. There's also likely going to be more focus on your final two years.
I would say that if this is something you're really passionate about pursuing - don't give up! Although grades constitute a good chunk of your application, other things will be considered too, such as your statement of intent, reference letters, and extracurricular involvement. Speak with an academic counsellor and/or professors at your school to get their opinion and advice.
I will be heading to NPSIA next year but I also got into BSIA (I didn't apply to Munk). If you have any questions, feel free to message me - I am happy to help if I can!