Make a copy of the graphics file in a folder named ExternalGraphics, and rename it to ExSpriteGFX00.bin
Place the swimming_goomba.ssc file in the same folder as your rom.
Then, pass the -ssc command line option to PIXI. Something like this in a batch file should do:
"pixi\pixi.exe" -ssc "swimming_goomba.ssc" -l  "pixi\list.txt" <your rom name>.smc
If the sprite still looks messed up in LM, open the Map16 editor, press Ctrl-Shift-PgDn, go to page 104, and from there, find the 4 messed up tiles. Take note of the numbers of the first and the last.
Then, finally, open swimming_goomba.ssc in a text editor, and change the two numbers to the ones you noted above. Save, reload your ROM in LM, and there you go!