This sounds more like a hardware problem, related to your USB 3.0 controller, or the controller in your USB 3.0 drive.
There’s really no such thing as “putting too much strain” on a hard drive. They’re meant for that. USB is plenty efficient these days. Yes, it’s true that USB drives can’t initiate transfers (technically speaking, Firewire drives can, as could SCSI before them). But basically what happens is that your PC starts a USB transfer, the USB controller uses bus-mastering DMA, just as Firewire or SCSI would, and as the transfer progresses, the USB controller interrupts the processor. This is, in fact, exactly the same kind of thing that happens with PATA and SATA.
And of course, on USB 2.0 drives, the link is slower than many drives, so you had lots of waiting. But there is no situation in which a properly functioning USB drive would just lock up. USB 3.0 is actually faster than any HDD is going to be, so it’s going to moving data faster. But it’s designed to do that, all day, every day. So if it’s the drive or the controller, that’s an implementation problem. First thing I’d do — update all USB 3.0 drivers.
Second hypothesis… maybe it’s not the drive. I know DNxHD is fairly hard core, size wize (usually 144Mb/s or so), so try a little torture test: put some uncompressed or Huffmann encoded HD video out on the drive. Beat it up just as you did the DNxHD. If it’s working, that suggests a problem with the DNxHD CODEC (which, last I checked, hadn’t been updated in ages) or Quicktime (running the latest version?). Anyway, places to look for a fix.
-Dave