I don't like the fact that Buildcraft pipes break when you hit them: I would like to give them maybe the same durability as cobblestone or something similar.
Is there a way to give buildcraft pipes some measure of durability?
As far as I know, this isn't possible. I think your best bet would be to surround them with blocks. If it isn't possible because there isn't room, I would move your buildcraft stuff to a seperate room and get output and controls somewhere separate. Kind of like how your plumbing is hidden from you in your house. If this is too much work, I'd say your only option would be to edit the source code compile and reinstall.