I know we are supposed to be using UNIX as a collection of tools but are there any big applications where I can run/test C programs without exposing the poor things to the outside world? 
If that's what you think an IDE does, I'm afraid you're mistaken 
Unless you put it in a chroot or something, they run with the same permissions and access the same things they always would. I've never found an IDE that does differently.
IDE or not, you may occasionally find the Data Dump Debugger useful.