Unfortunately, Vagante cannot currently be modded beyond visual changes, audio changes, some level generation, custom levels, and some attack values. As a result, modding the controls is, unfortunately, not possible at this time.

I've spoken with Ekun, the lead developer of Vagante on a few occasions, and he said that someday he would like for Vagante's modding to be more accessible and more powerful, but it isn't quite clear when or if we will ever reach this stage, as he is currently the only developer working on Vagante.

I hope you'll be able to play Vagante comfortably regardless, though, and I hope the lack of mouse controls on Vagante won't discourage you from playing an extended amount of time. You are not the only one who has made this complaint, so I wouldn't give up on it forever, but at this current period in time, it isn't possible. Sorry about that. :(

I hope I can help. I know this isn't the best option for everyone, but if you're willing to put in configuration time before you play you can use X-Mouse Button Control, it's a free software that lets you make mouse profiles per window. There are other programs like this one, and some even come with your mouse if it's a gaming model with lots of buttons.