From a conceptual perspective ignoring mechanics for the moment, I still have a hard time meshing these two base spells. The Gladius of Light "brings forth" the weapon. Whether you want to call it a summoning or manifestation of will it is external to the character. It's effect is inherent in the fact that the power has been focused at a point (the weapon) to generate the desired effect.
Body of the Warrior very specifically internalizes the manifested power, toughening the skin and hardening the body to grant the extra damage. If the two are combined then logically the gladius of light effect becomes a layer on top of the body of warrior effect. The result of that would be to sheath the character in a golden nimbus of light.
While an impressive visual effect, I think it would lose it's most potent punch. If you stab someone with the gladius of light and the blade ignores the defenses of the creature, it will bite deep. Striking with a hand that's coated in a very thin layer of the power means that the light might not even get through the being's armor or clothing before the hand underneath encounters the creatures substantial defenses. The spell wouldn't fundamentally change the nature of the person given the layering affect as noted above, so it's not like the light punches a hole in the defenses for the fist to follow.
To me this feels like the more correct approach. Especially given that the Body of the Warrior spell doesn't create a weapon, it simply strengthens the body to be more effective.
In terms of the damage, following the logic presented, my inclination would be to say that the non GoL damage would be assessed first against the creatures defenses for physical creatures so d4 (Mi) vs. AR. IF it would bypass, then the strike sufficiently penetrated to do damage and the secondary GoL effect would also count. If the physical strike did nothing, then neither would the GoL effect. For incorporeal creatures, the physical strike would pass harmlessly through it, so only the GoL damage would apply.
While a "realistic" interpretation from a rules perspective, it's also complicated and more confusing. It raises questions about what happens if you have a way to affect spirits physically, and then you've got to reassess as well.
I think for a home campaign you could find an explanation and balance that the GM and the player could agree on. Within the realm of the shared LoA campaign, I would be inclined to say this is a spell combination that's better avoided.
This thread has encouraged me to go back and review my Dark Blade of Illir (Twilight's Blade) spell to bring it in line with the current Errata. Very situational, but could still be fun.
As I mentioned the first time, I think it's a creative idea. In a home game I think this has more potential than in LoA.
If Matt doesn't have any objections to my interpretation about the complex interaction of damage and creatures I'd allow it at my table. Your mileage may vary from GM to GM though and would be worth checking in advance. The other thing I would note is that being sheathed in a brilliant golden light is impressive and is likely to garner a lot of attention. Still, if you're short a torch....
With a sweep of his hat,
Paul