I find that unlikely. First off, bill C-250 has not (as of yet) gone to third reading or a vote yet. Secondly, what the bill actually does is amend section 319 of the Criminal Code of Canada which is the section covering hate speech. This amendment simply extends existing hate speech laws to cover homosexuals. Restricting normal religious speech would also bring the law into conflict with the Charter of Rights and Freedoms, which would trump any such bill.
Also, this is a private member's bill, and it is more than likely it will come to a free vote anyways (ie. party discipline is not enforced).
It should be added that to be considered hate propaganda, the general criteria is:
a)advocates genocide
b)incitement to violence
c)group defamation
Under this criteria, only a bare handful of hate-speech prosecutions have ever been made. In addition, the decision to prosecute in each case must be made by Canada's attorney general.
Some info on the relevant Canadian law may be found at:
http://strategis.ic.gc.ca/SSG/sf02998e.html
Tokyopop might still decide not to rate gay materials, but it will come down to a business decison, not a legal one.
/*edit: Sorry, application of the law is the decision of the provincial attorney general, not necessarily the federal one (it's been a while since I've had to know this stuff)