I don't understand the options as being having pre-clearance or continuing to have pre-clearance. I have not heard any indication from the government that, had none of this happened, pre-clearance would have been withdrawn. As we understand it, this was a condition precedent to getting new pre-clearance at Quebec City and for cargo, none of which we quibble with as desirable things.
All that being said, the executive or the Queen is free to make her agreements, but Parliament isn't bound to do the bidding of the executive. Parliament is free, and in fact obligated, in fashioning laws, to ensure that they respect the charter. If the executive has concluded an agreement that, in its particulars, requires Canada to violate its own constitutional principles, or at least to create an environment in which those violations may be more likely, I think Parliament needs to take that very seriously.