I myself have wondered the same thing, and after some reflection I have concluded that the distinction, like a lot of other things, has to do with the framing. After all, literally the only difference between the scene where Peggy kissed Steve and the one that caused Peggy to shoot at him is the way the movie frames it. When Lorraine kissed Steve, ominous music started playing when her intentions became obvious, and it built up and didn't stop until the kiss was broken. And Steve was also given ample opportunity before the kiss commenced to express his discomfort. Meanwhile, when Peggy just forces a kiss on him out of nowhere, thus denying him a chance to object, heroic music is playing in the background: and while Steve does have a clearly uncomfortable expression on his face after the fact, his face is not focused on for very long, and the kiss is immediately followed by a lighthearted comment from Colonel Phillips. So the movie is very clearly trying to insist that Peggy's kiss was good while Lorraine's kiss was bad, even though there is not much difference between them. This drastic difference in framing has unfortunately fooled a lot of people, evidently.