Have you ever tried applying a grayscale filter to the Spectres, before the alpha channel change?
As I understand it, right now you use the same texture as the pinky Demons and adjust the alpha channel. But I think removing the color saturation entirely and going grayscale would make them harder to see and more in line with the original look and feel. This could be a game option (or just console variable).
As for coding the grayscale funcion in C, no idea. I was thinking of making a fork to try it out, but I think it's above my programming pay grade. I did find that there are various algorithms to convert to grayscale, with different "visual" results:
So would be interesting to see which one fits the Spectre better. (ignore the vb6 tho)
This would apply to any other partially invisible enemies in Heretic/Hexen? but idk, I don't play those. I guess it would apply to Marines in multiplayer if they pick the power-up.