Mythbusters Episode: "Piano Pile-Up"
I couldn't help but want to look up the details of the Mythbusters episode Alexander mentions in his answer. Here is the video, and here is the summary:
(Edit note: The Mythbuster video has been removed from YouTube, and I haven't found a replacement. However, there is this video which shows the same concepts - Even if it is just a bunch of people dropping a piano on a house for fun.)
A piano dropped onto a house built in the 1800's will smash cleanly through both the roof and the floor.
The Build Team found a one-story house slated for demolition, marked several target points on the roof between joists, and used a construction crane to hoist and drop various pianos from a height of 50 feet (15 m) above the roof:
An upright piano weighing 700 pounds (320 kg) damaged the roof but bounced off without penetrating.
A baby grand piano weighing 1,400 pounds (640 kg) pierced its legs through the roof but was unable to fully break through.
Calling the myth busted, the team loaded another upright piano with enough sand to reach a total weight of 2,600 pounds (1,200 kg), much more than a full-size grand piano, then dropped it from 75 feet (23 m) above the roof. This time, the piano did smash a hole in the roof and landed on the floor.
So, Alexander seems to be correct--your average house will not be damaged much by 50kg of poop. Houses generally speaking seem to be able to stand up to 24 loads of guano simultaineously on the roof before breaking.
To protect the houses from the intense winds generated from flapping of wings, the houses could have rock wall wind baffles around them:
This would send the intense winds up and over the roofs.