Wirelessly posted (Mozilla/5.0 (iPhone; U; CPU iPhone OS 4_0_1 like Mac OS X; en-us) AppleWebKit/532.9 (KHTML, like Gecko) Version/4.0.5 Mobile/8A306 Safari/6531.22.7)
To the OP, I understand your concerns, but I think that you're lumping a several different "do not want" items that are actually separate issues.
First off, if your device is jailbroken, Apple will find out if you bring it in. There's no getting around that. You can mitigate against that problem by regularly backing up and restoring your device should you ever need to bring it in, but that's about it. If that's a line you can't cross, well then "it is what it is. "
Side effects of jailbreaking (besides awesomeness, as pointed out earlier) do include the possibility of conflicts and problems. Being un-jailbroken doesn't guarantee zero problems either, but the chances are obviously less. My suggestion is to choose jailbreak apps carefully, avoid beta's and old Winterboard themes, (I had a bad experience with WB and swore it off altogether) and keep it minimal.
The impurity of a jailbroken iPhone is in my view, dependent of how far you've left the reservation. You can jailbreak and make your phone look like an Android/WinMo/iPhone conflagration that would give Steve a heart attack, but you could also keep it very close to original and just add a little bit of functionality. It's up to you. You don't have to jump into the deep end of the pool if you don't want too.
Security concerns worry me also, but that too can be mitigated against. Certain Cydia apps are downloaded by HUGE percentages of jailbreakers, while others are almost unheard of. By sticking to the well known stuff, you have a better chance of finding out if there are holes, and using your update function thru Cydia to get the updated version in a timely manner.
Let me wrap up be describing my jailbroken iPhone.
I've kept it pretty minimal. It looks like almost any other standard iPhone. In fact, if you didn't know that Notified or BiteSMS were from Cydia, or that the standard iPhone couldn't have five icons in the dock, you probably wouldn't think it was jailbroken. Lots of people like the customization of Winterboard, but I like the look and feel of standard iOS. I just wanted a little more, that's all.
"LockInfo" for a useful lockscreen with weather, and status bar icons.
"BiteSMS" for the super quick compose & reply.
"Notified" for great notification handling the way Apple would do it.
"My3G" for mobile FaceTime (oh the irony)
"ToneFX" for custom email and SMS tones.
"Fake Carrier" because " SEAN" is cooler than "AT&T"
"Spring Flash" just because.
Other tweaks (some are mandatory for above apps to function) include SBsettings, Activator, PDF patch, etc.
Sorry for the long reading, but hope this is useful.