The Charter actually applies to governments, and does not distinguish among the people it protects. Section 31 (1) of the Charter states that "This Charter applies (a) to the Parliament and government of Canada in respect of all matters within the authority of Parliament … (b) to the legislatures and governments of each province in respect of all matters within the authority of the legislature of each province. Since the Immigration Act is federal, falling under the BNA Act powers assigned to that level of government, immigration matters are all under federal authority, and the Charter “applies to the Parliament and government of Canada.”
Diabetes also counts as a disability. The issue actually has been addressed by some lower courts, as has the admission of a woman applying for immigration who had had breast cancer and was excluded on the basis that the cancer would likely recur, and this would put too much of a strain on the public healthcare service. In the diabetes case, the court argued that the law was consistent with the Charter since it was not discriminating on the ground of a physical disability, but was discriminating on the basis of the excess costs that the disability of diabetes would produce. But of course, this argument was ridiculous, since the discrimination on costs could not be avoided with a diabetic applicant, so it was in effect a discrimination against diabetics.
In its reasoning, the court made the same mistake as had been made under the 1960 Bill of Rights in the case of Bliss v. Canada (A. G.) (1979), where the court had held that an unemployment benefits statute that did not apply to women when they were pregnant did not discriminate against women, which could have violated the equality right, but only against pregnancy, and so it was acceptable. The Charter’s equality provision, s. 15 (1), was designed to avoid this problem, but we find it still being misread by lower courts to replicate the problem.