It will certainly effect the ability to evacuate the piping as the organic material will outgas. I can also decompose from heating releasing more contaminates and ruin the experiment.
I cant imagine something pulled by such a small animal can seal well enough to trap all the debris. The pigging method uses compressed air to generate a much higher force so a very tight seal can be made to ensure a clean scrub of the walls.
When they are determined, they are surprisingly strong animals. We had one pull a baby gate across our kitchen and living room because it liked the rubber stoppers and wanted to steal them.
Of course, the ferret was only pulling the string through the tube, but I wouldn't be surprised if it was capable of pulling the cleaning plug.