That is a good point, though the separatists themselves disagree, as they're still working to submit their own petition. I guess the question remains of how many times a petition like this can be made. If this one fails, can the separatists put forward another one? That's not going to be great. "Alberta couldn't pass a petition to stay but could pass one to leave."
Another thing to consider is our neighbour to the south. If the petition to leave passed, would they care that the threshold is extremely low, or that this doesn't actually mean that Alberta has separated? It's not like Trump has stopped believing that we should be the 51st state, and it's not like anyone in the American government cares enough to stop him.
A petition to leave passing might compel Trump to "little green men" us, because, y'know, we "voted" for it.
To be frank we're just in a really shitty situation.