Hi Lisias. In this case, no it is not cheating and it was for a personal game. I based my advice on the image provided, which showed the probe payload seriously clipping through the shuttle cargo bay. As all that would be done was shrink the probe down without changing anything else, all that would be happening would be size times mass, making the probe more dense. No easier for the shuttle to lift into orbit and the same calculation of thrust vs mass in a vacuum for the probe to move itself. No lifting surfaces to be affected etc. It also wouldn't affect anything else in their game nor do anything to damage their save games.
I love TS and all the hard work you do, but in this specific case, it was a valid workaround for the situation.