I understand Northern Dancer's point. I think that at this point M-T/M are normally a significantly better team than D/W, and certainly the international judges think so. Furthermore, it is a strange situation to see a team that just missed the Grand Prix final not competing at Worlds.
However, perhaps the premise that a combination of D/R and M-T/M could get three spots for next year is questionable. It's possible, but IMO not very likely. If that is true (my assumption), then the rationale for sending M-T/M rather D/W is not very pressing. On the other hand, barring disaster a team of D/R and D/W is just as likely to earn two spots as a team of D/R and M-T/M.
Therefore I don't see why Skate Canada should have ignored their normal protocol in this case. M-T/M should be fine in terms of assignments for next year, since they should finish in the top twelve in terms of season's best and ranking. For D/W, the assignment to Worlds could help them in that regard.
For M-T/M it could even be a positive thing if they handle it correctly. For one thing, it gives them more time to prepare for next season. Also, it gives them the experience of having a disastrous competition in a situation where the cost is not as great as (say) at a Grand Prix competition or at Worlds. If they can figure out what happened and learn how to prevent it in the future, it could end up being a very positive thing for them in the long term.