Just taking a gander at this topic, but perhaps a way to test for IC systems might be to focus on the genome instead of the systems within a cell instead?
Instead of focusing on removing individual "structures" within a cell focus on the genome. What i'm trying to get at maybe form an experiment where you systemically cut up a cell's DNA and resplice it together and do it at a numerous variety of positions in a variety of sequenses and then cut it down until the cell no longer functions. Then take a look at the least "functional" cell and see what it has.
My knowledge in this particular area is minimal and i've no idea if this type of experiment is even feasible, i'm just throwing something out there for discussion sake, sides it sounds more objective then any real description of IC system i've heard of so far anyways.