I guess technically it shouldn't matter if the textures aren't p^2, just so long as the sheet is.
That doesn't make it any easier for asset management however.
I think the best solution would be to have the 2px padded images on their on sheet, one that didn't need to tile.
The other options are the ability to turn off sprite sheeting, turn off the 2px padding, or give the user the ability to make their own sheets.
The last being the least likely since it rules out the padding thing.