I've never heard of a filter current blowing a fish's fins out. Pinholes can be a sign of strain though, so that makes a little sense. The extra flexing and movement of the fin, like what happens in flaring definitely can cause pinholes. I can understand how constantly fighting the current could put strain on the webbing, however, I would expect this to look similar to injuries from "blown" fins from too much flaring. It's possible that it is a combination of biting and blown fins since the current can be very stressful, as well, and that can be a trigger for biting.
Anyway, the solution I came up with for my Eclipses was to take out the biowheels and fill the biowheel compartment with either porous gravel or ceramic filter pieces. Then I put pieces of 50 micron filter pads on top of the gravel. This baffles the flow and provides a lot more surfaces for bacteria to colonize. After all, biowheels are mostly just a gimmick. They're designed so that when you replace your filter cartridge, which you shouldn't do, you still have bacteria in the biowheel.