The Galaxy S II doesn't have a locked bootloader, so DavidAP's (deleted) post doesn't really apply in this case. It's also theoretically possible to exploit a flaw in a bootloader or something and re-lock it, though I don't know of such a method. But anyways.
As noted here, it may be possible to fully back up a Samsung device through Odin, though we haven't been able to get it working. Doing so would allow you to backup your stock ROM and restore it in perfect condition. Via Odin you can also flash a stock firmware image, completely obliterating any trace of rooting. This also might not be perfect, depending on where you get the firmware image — some of them are re-packed OTA updates and so on, and different from any "real" Odin package Samsung might use internally.
The problem is not with the real data on your phone, though; as noted it's easy to go back to stock and leave no trace of rooting. There's a counter that gets incremented when you flash your phone with Odin. It's possible to reset this counter, but that increments another counter. Samsung does check this counter sometimes so you should flash with ClockworkMOD or Mobile Odin to avoid that.
If you brick your phone, that's certainly your fault and I wouldn't expect help from the carrier/manufacturer. If you need them to fix a cracked screen or something I wouldn't expect them to care about any flashing you may have done, though who knows. That said, I of course am not encouraging you to void your warranty; that's up to you.