Now ... imagine that there were at least three stories a day about people being killed by malfunctioning Toyotas and then we found out that Toyota was using its onboard electronics to record everything everybody who rides in them is saying, to be used against them in the future, and remotely detonating a few of them every few days. Most people still get from point A to point B, but still a bunch of people are getting killed because they own a Toyota.
A car analogy, eh? Alright then, try this one on for size:
Let's pretend the company in your analogy were Mitsubishi instead of Toyota. Mitsubishi is a huge conglomerate that makes bunches of different things; automobile manufacturing is only about 10% (by revenue) of what it does.
We'll continue to imagine that Mitsubishi Automotive is still doing all the nefarious things listed above -- being really, really pissed off at Mitsubishi Automotive would still be perfectly valid.
There's also a division of Mitsubishi that makes pharmaceuticals (Kyowa Kirin). Let's imagine for a moment that Kyowa Kirin does something really great -- maybe it makes revolutionary vaccines that cure all the worst diseases, and then distributes them worldwide for free, for example.
Would you also be justified in being pissed off at Kyowa Kirin for Mitsubishi Automotive's actions, even though Kyowa Kirin had no control over them and the work it was doing itself was valuable, just because they had the same corporate ownership? Of course not!
And condemning the FCC just because the US Marshals fucked up makes just as little sense.