There are a few points in play here. First, during the period you were self-isolating, you should be paid your normal wages for the time you worked.
Second, under human rights law, employers have a duty to accommodate their workers. That includes accommodating a disability. But workers also have to be flexible, especially if you could only complete some, and not all, of your work from home.
As well, under the law, employees can take unpaid, job-protected leave due to COVID-19 reasons. This includes if they’re required to self-isolate after returning from abroad.
We'd suggest writing to your employer and let them know how you feel. Remind them that you had no choice but to self-isolate, and that you were still productive when working from home. Assess your productivity during that time, and ask to be paid your normal wage for that amount of work instead of using paid sick days. Be firm, but polite.
We've got resources on guiding you through problems at work, including tips for talking to your employer and writing a letter. If it can't be worked out amicably, we can teach you how to file a formal complaint.
Want to learn more about your legal rights during the coronavirus pandemic? We've compiled responses to the most common questions people are asking.