Laws made under the act are subject to the charter unless they invoke the non-withstanding clause.
Furthermore, have you read the link you sent? The entire "Provisions" explains while this is way out of line to deal with protesters in Ottawa.
Using it for "Public Order" as Trudeau is doing, was meant to be a tool against:
"The Act references the definition provided in the Canadian Security Intelligence Service Act, which includes espionage, sabotage, detrimental foreign influences, activities which support the threat or use of violence for a political, religious or ideological objective; or those activities which threaten to undermine or otherwise destroy, or overthrow the Government of Canada."