What is the problem? Just delete any triangles with edges that are long. Since the CRUST code will span that hole, any triangles crossing the hole will have at least one long edge. Zap them away. Problem solved. All you need do is decide on a parameter for how long an edge needs to be to want to delete the corresponding triangle. Surely you can do that much?
load pointcloud.mat
plot3(p1(:,1),p1(:,2),p1(:,3),'.')
So, knowing the hole on the bottom is what you wish to zap away, I would guess that any triangle with an edge longer than something like 5-10 units will let you kill off the offending triangles. 10 units may be a little too large. 5 is probably adequate. A quick experiment would allow you to choose something intelligent, based on your own eyes.
