I don't use the Pegasus now, but I did enjoy its silliness when I flew one for a short time.
I feel a lot of what made it problematic when equipped with Hurricanes, is the Hurricane weapon system itself. The second stage missiles are pretty tanky, making them hard to shoot down. This leads to situations where a missile classified as a 'Finisher' is actually just a stand-off weapon with limited ammunition. At the very least, that's how I see the AI use it, and read about players using it. I realize the classification is pretty fluid with any weapon depending on how you use it, but it might be a lot easier to examine the Hurricane than tool around with the Pegasus itself.
I'll admit that I'm a bit biased against the Hurricane, I don't like the weapon system in its present state very much. I feel it has very "nuh-uh, you can't shoot THESE missiles down!" vibes, which is strange for a high explosive two-stage MIRV. The Squall is a lot more palatable when you consider it's just a cold-launched rocket with a solid body. Breach SRMs also gave me similar vibes when they dropped, but they're also a lot more palatable when their full damage is reserved against armor, and I've grown to like them as a specialized tool for certain ship configurations.
RIP Pegasus, I don't think the problem was you, it was a missile named after a weather phenomenon.