I doubt it was caused by the pond turning over. Water temperatures in the depths are still cold this time of the year. Water at the surface is not that hot yet.

Yes rain water is cooler than the top surface waters and the lower air temps will cool the surface a bit. Remember that cold water sinks and hot water rises. There will be some mixing in the upper 10 ft in that pond.

A lot depends on how deep and large the pond is as to when or if it turns over. But remember it has to Stratify first. I'm wondering if there is a stong thermocline in May? It's been hot here in S. IN for the last week but it was cold before that. Highs were in the upper 80's and lower 90's for a few days in a row.

Perhaps lighting stuck the pond and killed the fish? Perhaps it's the threat of lighting striking the water that send the fish deep into cover after the storm arrives.