The index.html file is part of your project, given that no matter how you output it, the game is, at its core, an HTML5 project. You can go ahead and remove the music. I would still suggest just making your game and stripping it down later. Note that the HTML5 one will only use the m4a music and sound files, while playtesting will need the ogg files.
I was able to, through MV Stripper, resampling music files and resaving graphics files with higher compression, able to shrink my own project from around 500MB to under 200MB, and that is a PC distribution.
Why does your project need to be under 50MB? That doesn't seem like it will allow for much of anything in terms of an RPG at all.