You are quite right that a significant proportion of a realistic population are likely cripples, blind, etc (perhaps, not dwarves?). However, remember that the game mechanics are not really trying to be a model of a realistic population. The game mechanics are a model for the characters who are "significant" to varying levels in the story that the troupe is telling (and for identifying that level of significance). So, while it is perfectly true that a non-zero number of random peasants are cripples, most peasants are not characters in the story that the troupe is telling.
If a character in your story is a cripple, then that is (or should be) significant because it changes how the other characters have to travel, whether the group can easily run away from danger, etc. So, that character should be a companion (or a maga!), because she has a big impact on the story. She might well be a peasant too --- companions can be peasants; just give her an appropriate Social Status.
Of course, if your troupe really wants to give a grog a Major Virtue/Flaw there is nothing to stop you from doing so. The rules/guidelines are just trying to help you create a "balanced" story where some characters (companions and magi) are "important characters" and other characters (grogs) are "extras". "Companion" doesn't mean noble and "grog" doesn't mean peasant; the categories are about the character's "importance" to the story rather than necessarily the in-character social status/power of the character.