P.S. Ducky and Spike got stung by killer wasps in movie 6. I often look as the bee sting being the turning point of 2 sides---one side is the innocent days when they didn't know real pain. The other are days that are just as innocent on the outside, but with terrible knowledge within. 
First off, those weren't killer wasps. I don't think the term "killer wasp" or anything remotely like that was mentioned, nor was it indicated. If you mean killer bee, again impossible. Killer bees are hybrids, a combination of the hostile african bees (hostile because of more predators) and honeybees (less aggressive). They were bred like this for cultivation purposes. They didn't exist millions of years ago. If they were killer bees, then Ducky and Spike would have needed to run much further as killer bees, like african bees, will pursue their 'enemies' much further and are more relentless. So many individuals would sting them that there would be a reaction, or worse death.
Second, they experienced pain before the stings. Remember when Ducky hit the water in LBT4 so hard she was knocked out? The water is still a solid matter. Provided it's not that solid, but still solid nonetheless, and it still would have hurt. And it knocked her out and she almost got eaten because of it. That is more severe than a measly sting on the nose. Yes, that is painful, but it's not going to really impact her that much in anyway except make her nose a little sore. The falling and hitting the water hard enough to knock her out? She almost died because of it.
And let's not forget the rock slide they were in. All those rocks smashing up against her, which would have undoubtedly happened, would have been far worse than a sting.
As for Petrie, one other time he got hurt was in the first movie. Actually two times that I can think on top of my head. The first time is when he first appears. He hits the ground so hard that he cracks the ground. Now keep in mind, this is solid rock. It's hard enough that Littlefoot walks on it just fine, and he's heavier than Petrie, who is probably the lightest of the trio here. Yet he flies so fast he hits the ground and it breaks. The pain he would have felt would have been more excruciating than a bee sting, I can tell you that now. You could argue that it was a thin point in the ground, but it is still solid rock and it's probably heavier, or the same weight, as he is.
And the second time would be the fight with Sharptooth. He was snagged by razor sharp teeth, which, even if they didn't cut him, would have caused some amount of pain, and these were bone crushing jaws, not the puny stingers of a bee or wasp. And to add to that, he plunges into the water with Sharptooth and, in an unseen moment, pulls himself free. While we don't see it, there's a chance that he would have hurt himself because of this. Maybe I'm looking too deeply in this, but I'm certain that Petrie felt some pain worse than a bee sting from this, especially since Sharptooth grabbed onto a relatively thin part of his body, which was his wing membrane.
And even if that didn't hurt him, the bits of rock from the fall sure would have. I find it unlikely that he escaped all of these fragments given his location upon hitting the water. While they probably weren't bad enough to knock him out as evidenced by him getting out of the water soon, it still would have caused some pain, and worse than what I'd think a bee sting would do.
I don't really believe a bee sting would have "ruined their childhood" even if it was the first pain they experienced (which is false of course). I got stung when I was a kid, but I didn't go bawling and saying how my life was ruined. A bee sting, and a wasp sting, is just that. It is painful and it is unpleasant. But it's not bad enough that it is mentally scarring. I think Ducky and Petrie treat stings the way I usually see them treated: as minor inconveniences. Yes getting chased by a horde of bees is scary, but from their behavior afterwards, I think it's a safe bet that they took the stings less seriously than you are.
