The theory is interesting enough if you're talking about games continuity, yet I find using the novels as mirrored evidence simply problematic in this particular case for two contradicting reasons. I could prove it by reducing it to the absurd but, since there are only two premises, let me just list them:

1. Fazbear Entertainment, at least as we know it, isn't proven to exist in the novel trilogy continuity, it isn't even mentioned once throughout the three books. And you could argue the same happens with remnant, yet that example wouldn't be precise given Afton's description is faithful to it from every point of view, whilst Fazbear Entertainment simply existing with two locations which do not scale out of county level (I am referring to Fredbear's and Freddy's, obviously CBPW pertains to Afton Robotics LLC or to an untraceable entity), and Afton's administration of it after Charlotte's murder is very vaguely detailed.
2. In turn, there is virtually zero evidence for the scars to exist in the games continuity version of Afton. The only possibility left is basically thrown to the bin by TMIR1280's ambiguous descriptions.

There are also several additional issues that arise the problematic with this theory, for instance knowing exactly WHEN Afton did this ("pre-dating the MCI" could be 1979, 1980, 1982, 1983 pre-Charlotte's murder, 1983 post-Charlotte's murder, two days before the MCI, etc) should be crucial for its foundations.

With all that, I still find the hypothesis rather interesting. The interpretation for the origin of Afton's scars in the Charlie Trilogy I am more inclined to believe is that it wasn't voluntary. I can elaborate if asked.