On Parliamentary Supremacy
Parliament cannot, for example, violate the constitution. It could introduce a law permitting slavery, but that law would be rightfully struck down by the courts as illegal vis-a-vis the constitution. Further if the federal parliament enacted a law requiring school prayer, it would also be struck down as that is ultra vires the federal parliament, education being a provincial power. Parliament also cannot violate its own rules. For example if a procedure for amending a bill is set in the rules, ignoring that procedure makes the amendment illegal. That being said, parliament can alter its own rules. So to use a different set of rules parliament would first have to vote on implementing the new rules, then use the rules to move forward.
So the question is can legislation bind future parliaments? Strictly speaking no, but here's the rub, parliament must obey the current law in changing the law. So if a law has within it a mechanism for changing the law, parliament must follow the "manner and form" of current law. In other words parliament can't break the law to change the law. This is simple rule-of-law stuff that the Harper government seems to have issues with.
Which brings me to the CWB ruling. The government lost the ruling in that the court saw that the manner in which the changes were brought about was in violation of the current law. The new law wasn't struck down for the simple reason that it isn't law yet, however if the current ruling stands, the new law will likely be struck down as this court ruling provides precedent that the new law will be illegal.
Which begs the question what is Harper doing? Surely the phalanx of lawyers that work for the federal government would have told them that the current court ruling was a likely outcome. Further they would probably advised Harper and his cabinet that the simple way to avoid the problem would be to amend the current act to remove the change provisions. Let me repeat that. The simple way to avoid the whole court challenge thing would have been to simply amend the current CWB act to remove all references to plebiscites for change. This would have then made it legal for parliament to unilaterally disband the CWB without any input from anyone. It would have pretty much ended the protracted and expensive legal battles that will now plague the government and agriculture for the next few months.
So why did Harper choose this path? It is well known that the Harper regime is famed for ignoring the often good advice of those who work for them in order to pursue a purely ideological path (or just to do something brainlessly stupid). This could be the simple reason. The Harper government just simply ignored what would have made the process a slam dunk because they were simply ideologically blind and in a rush. Another more sinister take would be that Harper is purposely taking the hard road. By taking this path Harper's ensuring that the buttons of his followers are pushed against "activist judges" and a likely war on an independent judiciary, the only check against the abuse of power by the government is begun.