What else would they have been used for?
What would you have done with them?
Burn them? Seems disrespectful, as do any other ideas I can come up with.
This isn't exactly something that a University (or any group, for that matter), has to deal with every day. There is no rule book or a set of guidelines on how to handle the situation.
The way I see it, what was done with the logs was the right choice. It's not something you want to draw attention to, like "hey look what happened with these!", makes it seem like some sideshow tourist attraction. It's not something we want to forget about, either, had they been disposed of. Instead, they are quietly tucked away, off the beaten path. They serve as a grisly reminder of the tragedy that this University suffered. They are but a small piece by which we can remember what the families, friends, and the University as a whole lost in 1999. They are not a shrine. They are not a memorial. They are not a sight meant to be seen. They just are. Leave them be.
Just my $.02.