Ethically speaking, I'd say that your present guilt at not having felt guilt in the past speaks positively of your own moral character.
As it turns out, you did not in fact have reason to feel guilt in the past because you had not injured another person. Nevertheless, to feel guilt when you (believe you) have injured another is morally valuable. For one, such guilt indicates a recognition of your own wrongdoing and is evidence of your moral knowledge and perceptiveness. And from a more consequentialist or utilitarian point of view, being susceptible to guilt encourages us not to injure others. After all, guilt feels bad, so being susceptible to guilt is good inasmuch as the desire to avoid justified guilt should engender a desire to avoid injuring others.
The guilt you're feeling now is what philosophers such as Harry Frankfurt call a 'second-order' attitude: Your present guilt is directed at (or we might put it more technically, has as its object) your earlier lack of guilt. It is an attitude toward one of your own earlier attitudes. That may seem odd, but in fact second-order attitudes are very common. We often have, for examples, desires regarding our desires. I might desire mocha brownies, while also desiring that I not desire mocha brownies. They're not healthy for me after all. In fact, your present guilt can be seen in precisely those terms: You feel guilt now because you desire to have had different attitudes in the past. But the fact that you feel guilt now is a sign of moral maturation on your part. Your attitudes toward your own actions and judgments are becoming better aligned over time.
So in short: Don't worry -- feel guilty. At least for a little while!