While I wouldn't want anyone to pad a story, is there perhaps an way of expanding the piece? Not just to make the word count, but to create something that is more complex eg the addition of a subplot supporting the theme.
I don't know why the 3,000 words minimum was chosen for the original Distaff, but it seems to me to be about right -- I think it's a good idea to elevate the stories beyond flash fiction into something more substantial, so the anthology has weight, literally and figuratively.
Whether we could accept one story so far under the limit might depend, though, on the word count we have for the others and whether the total would appear to give value for money for anyone buying the anthology. I've no idea if there's a sweet spot for word/page count and/or number of contributors.