In theory you could actually modify a jar file with the LC ZIP functions. A Jar file (such as mine craft.jar) is just a zip/rar (not sure which) file with a different extension.
You could therefore open it with LC, do stuff and save it (close it) as long as you can do so without losing the .jar extension on the way. You could rename the file temporarily if needed.
Look in the dictionary for: revZipOpenArchive, revZipAddUncompressedItemWithFile, revZipDeleteItem and revZipCloseArchive. There are more than these, but you should check these first.
LC cannot modify the compiled Java files inside though - that is not something you can do unless you have the actual sources.
But, while testing, DEFINITELY make a BACKUP. Don't even play with the jar without one. If it breaks then it's not likely you can glue it together again.
With the minecraft.jar you are probably wanting to delete and replace files inside it (for modding) and then remove the META.INF file too

As you can probably guess, I'm also a MC player
Let us know how it works if you get anywhere.
Cheers,
Dave