Just because there is a lack of 
proof, does that provide 
sufficient evidence to suggest they
are from domestic colonies?

The burden of proof rests on you. In science, we deal with probabilities. For example, you may show me a rock and state that it fell from the sky, that it is an extraterrestrial rock. I say that probably it's just some old rock. Probability is definitely on my side, there are plain old rocks everywhere, anyone can pick one up and says it's an ET rock. You are going to have to show that it has some identifying quality that makes it much more likely that it's a meteorite. 

Same with a colony of bees. There are domestic hives by the thousands, they saturate they area with drones, any queen that goes out, feral or otherwise has a 99% probability with mating with these drones, so that resulting colony is 99% likely to be derived from domestic stock. Further, all honey bees in the USA are derived from domestic stock, imported from Europe. In order for a distinct population to arise it would have to be isolated by *some factor*. 

If you could show that the feral colony was distinct in some way, and demonstrate how this could happen, then you would have a case. For example, in Landes, France there is a population that appears distinct and Jamie Strange went there to study how it could be, with commercial stocks all around. The theory was they had an annual colony brood cycle adapted to a local flora, leading to differential mating patterns.

QUOTED
> Colonies from the Landes could be differentiated from non-local French A. m. mellifera populations using morphometric analysis, and from non-native and reference populations using mtDNA and microsatellites. Seven morphological characters were identified by discriminant analysis as informative for delineating the Landes ecotype from other A. m. mellifera populations. Mitochondrial haplotypes for the population were characterized and five microsatellite loci were found to be informative in characterizing the Landes population.

from "Morphological and molecular characterization of the Landes honey bee ( Apis mellifera L.) ecotype for genetic conservation"
J Insect Conserv (2008) 12:527–537

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