You can delete files in an MPQ with MPQ2k. This is how it should be done.------------------------------------
4.7 Deleting Files - the D Command
One of the other useful commands in MPQ2K’s arsenal is the delete file command. The general syntax for which is:
MPQ2K d <MPQFile> <FileToDelete> [/r]
The parameters in <> are required, ones in [] are optional. FileToDelete is just that, the file(s) to delete; and, as usual, /r tells MPQ2K to recurse through subdirectories.
The first time you use the delete command, you might be rather surprised to find that a deleted file rarely takes up less space in a MoPaQ than a file that hasn’t been deleted! This is due to the fact that the delete command only marks a file as deleted; it doesn’t actually remove the file from the archive (to preempt the next question, no, you can’t undelete a deleted file). To actually remove the file from the MoPaQ, you must use the flush command.
4.8 Flushing Out an Archive - the F Command
As mentioned above, the delete command does not actually remove a file, rather it only marks a file as deleted. Obviously, there must be some way to remove files from an archive, or else the delete command would be utterly useless. As a matter of fact, there is a way, and that is the flush command, using the following general syntax:
MPQ2K f <MPQFile>
All parameters are optional. MPQFile is the file to flush.
The flush command searches through a MoPaQ and purges the space deleted files occupy, shrinking the MoPaQ’s size if there are any deleted files in it.
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The above was taken from the MPQ2k manual.
BTW, putting files into MPQs is a thing of the past and outdated. Its also a pain in the @rse to pack files into MPQs. -direct -txt rulz nowadays. 
[This message has been edited by BMW (edited 20 February 2002).]