I'm certainly not going to defend VIA for not having contingency plans in conjunction with CN - this type of thing seems to be hardly an isolated incident for them.
But . . .
It's not always as easy as it seems. This was not the only stranded train, so maybe their ability to send a rescue train was hampered by other causes. Could it not move because of the tree or was it not allowed to move by RTC?
If they want buses on stand-by, they would have to pay for it. School bus companies would have to find drivers; where would coach companies have to come from. My brother used to driver for Trentway-Wagar and did the odd run to Sudbury to get Via passengers - from Toronto. On a night like that, would a bus company even allow their fleet out? The fact that it is on the Kingston sub doesn't guarantee that every part is road-accessible. I understand this one (55?) was, but probably not all were. The proposed route for the HFR has a lot of inaccessible stretches so I'm not sure it would necessarily fare much better except that all decisions would be VIA's (not necessarily a guarantee of a good thing)..
CN trains were also stranded, but their concern is purely economic.