Now that you mention it, this may not work with Project:M since (I think) it replaces FitFalco.pac, which is where his moveset changes are implemented.
Out of curiosity, I compared the files in the download I linked and the original Brawl FitFalco.pac. There are countless small hex differences that one could implement in Project:M's FitFalco.pac to change the laser color if one felt like spending a day or so replacing blocks of hex code. Outside of modifying the hex code directly, though, I don't know how to change his laser color.
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Edit: I took a look at Project:M's FitFalco.pac in BrawlBox and managed to change most of Falco's laser effects from blue to red. The little spark at the tip of his gun is still blue, but the laser itself and the blast ring are both red.
Here is a download link.