You would use pywallet, see here to delete a specific tx:
https://bitcointalk.org/index.php?topic=34028.msg2239679#msg2239679

pywallet.py --multidelete file.txt [--wallet wallet.dat] [--datadir /bitcoin/directory]

Your file.txt would contain the tx's, one per line or you could do:
tx
all

as contents of your file.