Not sure I understand the question. Once you've keyed the sd footage, you're free of the constraints of aspect ratio. Your composition resolution should be based on the widescreen footage. By the way, when you say widescreen, do you mean HD 16:9, or SD widescreen?
In either case, there should be no "black bars" to speak of.
But if by "chromakey footage" you mean that the shot has already been keyed and composited over a background plate, then it seems that your main comp should be 4:3 SD letterboxed to accommodate the widescreen material, be it HD scaled down or SD.
In this scenario, you create a 4:3, 720x480 comp which fits the non widescreen shot. Drop in the widescreen footage and scale it so that it's letterboxed inside the comp. This letterboxing will be your guide to create a masked solid above for the non widescreen material, so that it has the same letterboxing. You can change its position vertically for the best fit.
Now you can intercut it with the widescreen shots, but your finished piece will be letterboxed throughout.
By the way, if you're not needing any additional compositing or fx work, all of this can be done, I'm sure, in Vegas.
I do not understand the problem- you have chroma in SD, you key out the color of the chroma and you get a subject with alpha. You composite that on top of widescreen bk and you get a widescreen final composite.... where do the black side columns come into the picture?