It doesn't make sense to say that something predictable and cyclical is a bad omen. It's like saying the seasons, which occur every year, are a bad omen. The case of eclipses are just further apart.
The achronim assume Chazal knew what they were talking about when they said מאורות לוקין, and assume that they knew how to predict eclipses (I'm not sure if that's the historical consensus), so they want to give a different explanation of that gemarra.
One is the Aruch LeNer Sukkah 29a. He felt the term "בזמן", at the time of, was extra. They should have just said when חמה לקה. Rather it's referring to the time period when the eclipses occur. Yes the phenomenon is predictable, but Chazal knew this specific time was a time of דין, judgement.
The other is the Yearos Devash, Chelek Beis, Drush 12. It's referring to something that sounds like sun spots. Some blotch on the sun blocking its light (although I'm not sure how to this would be true for the moon).
You could also say it's referring to something that doesn't occur anymore, but I don't know if any source suggests that.