The following is by no means a definitive accounting of the political and legal considerations that might be at play, but, having spoken with a few legal scholars over the last day and a half, the federal government would seem to have at least a couple options should it decide to challenge Quebec’s charter of laws.
First, let us dispatch with the option that exists on paper, but is almost definitely not feasible: disallowance. The Constitution Act of 1867 gives the federal government the power to disallow any Act passed by a provincial legislature, but this power was last invoked in 1943 when the federal government blocked Alberta’s Act to Prohibit the Sale of Lands to any Enemy Aliens and Hutterites for the Duration of the War. The power has since fallen into disuse and invoking it now would likely precipitate a constitutional crisis.
That leaves at least two more reasonable options.
The federal government could refer the matter to the Supreme Court: Section 53(1) of the Supreme Court allows that the “the Governor in Council may refer to the Court for hearing and consideration important questions of law or fact concerning … the constitutionality or interpretation of any federal or provincial legislation.”
Or the federal government could seek to intervene in one of the challenges that would be likely to be filed in Quebec against the charter should it be passed into law.
A bit of history: In 1977, Pierre Trudeau chose to not challenge Bill 101. John English’s Just Watch Me covers the situation here. In his memoirs, Mr. Trudeau explained as follows:
Yet, however much I philosophically disliked Bill 22—and later the Parti Quebecois’s even more stringent Bill 101—I had no intention of using the constitution to disallow the legislation. The way to change bad laws is to change the government, rather than using Ottawa to coerce a province. The best course was to hope that Quebec citizens would challenge the provincial legislation in the courts—which happened to several discriminatory provisions—and to hope as well that the people would become better informed and their politicians more open-minded.
According to Ian Brodie’s Friends of the Court—see here—it was when such challenges did not emerge that Mr. Trudeau’s government launched the court challenges program.