On the pond tour yesterday, a guy had a similar situation. He had a fairly deep reservoir where the skimmer went into. His solution was either:
1. The skimmer net was large enough that the fish could survive swimming around in the receptacle, until he fished it out the next day or so.
2. Or, the net had a hole in the bottom, allowing the fish to get into the reservoir, and the junk that floated was still floating in the top part of the net. In this scenario, it's possible he had even rigged a hole from the reservoir to the pond, down low, to allow the fish, but not the debris, to make its way back into the pond.
Sorry I didn't get full description, but that may give you some ideas.