I use AE and it works real well---just save as AVI file and import into Vegas---WIth Vegas and After Effects I have in my mind the perfect marriage of NLE and Compositing.
Commotion (in my limited experience) is also quite good. The workflow is exactly the same as with AE-- export as an uncompressed .avi file, import into Vegas.
And AE (which I have a bit more experience with) is also pretty good. Not quite (IMHO) as good, but it will get the job done...
I thought Commotion was strictly Mac based. Has that changed?
Again, does AfterEffects have drawing tools? How do you select the wires to be removed? and how do you paint around the "good stuff"?
The last issue of DV (dv.com) has a feature about special effects -- not the sci fi stuff -- including some info on wire removal that may be of interest.