First of all, "Who Owns
Whom?"
In answer to your question, hell yes. While deniable assets (a.k.a. shadowrunners) are often more desireable than corporate employees when taking action against another corp, they are absolutely vital when taking action against your own corp. And if you are pulling some kind of inside job, might as well pose as your enemy and see if you can get them in some trouble while you're at it. Many times I have had a Johnson drop clues that they work for a company other than what they do. That way, when the runners pick up on them they think they're brilliantly clever when they're actually falling for his ruse. Plus, when an inside job goes bad it's way more entertaining than a regular job.
Realistically, though, (that's SR-realism, for you kiddies following along at home) while only ten corporations own probably 90% of everything, two branches have to be pretty close to each other on the "corporate family tree" to really have anything to do with each other. Using your example, a run on the Peace corporatoin would affect cereal production and Golden Temple, but the security services that are owned by a guy who owns an group that owns Golden Temple would not be affected in the least. They might as well be seperate corps.
edit: I'm just being a smartass with that 'whom', thing. Ignore that part.