Ah, I had misunderstood your usage of USB booting; I hadn't realized you
were using an USB cable to push a clean bootloader.  (I guess you took
care to patch your bootstrap bootloader to ignore uEnv.txt and basically
anything coming from the SD?)

Indeed, one option for you is to have a netboot image to wipe the SD card, then 
launch d-i, but I think you have at least two easier options thanks to 
preseeding:
* preseed a command in either preseed/early_command, partman/early_command that 
wipes the first partition or al files in the first vfat partition (up to how 
far you trust the SD card's contents)
* preseed partman to actually repartition and reformat unconditionally the SD 
card on every install

Would this address your use case?

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https://bugs.launchpad.net/bugs/961174

Title:
  flash-kernel fails to override uEnv.txt

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