ummm...no...I've flown into a few class B airports...sleepy ones...with my 182.
And I've flown into a few busier ones (ORD, ATL, HOU etc.) in "the company plane" back in the late 90's and early 00's. At that time the company plane was a P Baron. And that was disruptive enough. I would never consider it in a slower single.
What I am clueless about is why anyone finds it fun or a challenge. Give me a 1200' grass strip for a challenge any day.
One thing that I don't think has been discussed yet is that it's possible that you'll have to wait queued up in a line for a long time to take off...with jet fumes blowing in your face the entire time...on a hot summer day in Atlanta. Yeah, baby!!! That's my idea of fun!! Experienced that quite a few times in the Baron. Oh, it was great!
I've flown into airports like this probably 100 times or more in the 172 or 182, across the US and internationally, and not once has it caused any disruption. JFK, EWR, BOS, SFO, IAH, IAD, Lagos, Cairo, Cape Town, etc etc. Oddly enough, the controllers do know what they're doing, and aren't going to put a little GA airplane somewhere it'll mess up their main traffic.
The only time it would cause disruption is if the GA pilot isn't up to following ATC's instructions correctly and promptly; and you're right, pilots like that shouldn't be flying into these places. Maybe your company pilot was a bit behind things or out of practice, and ended up getting in the way.
As for departure, 9 times out of 10 they'll send you off a different runway without a wait, or cut you in front of the queue at an intersection, turn you out low level, and you're gone in seconds. If you do your homework about which runways and arrivals and departures are in use, and are ready to ask specifically for what you want and makes sense, you usually get it. Coming across as properly prepared and competent on the radio makes all the difference.