Well yes, that would be putting the amount of games he's missed into a relevant context. What other method could be used to demonstrate a player's non-injury proneness?
AFAIK There is no accepted figure of missed games that are required to be injury prone so the closest we can come to disproving its applicability to a particular player is to show how many of his contemporaries it would have to also apply to in order for that to be the case.
1st coice PL CBs that missed more games than Vlaar last season: Turner, Lovren, Tomkins, Chico, Cahill, Kompany, Coloccini, Demichelis, Bassong, Jagielka, Chester, Collins, Hangeland, Vertonghen, Turner, Dawson, Huth, Ferdinand/Vidic/Jones/Smalling (not sure who was first choice).*
Essentially, this has become a purely semantic debate now and demonstrating that Vlaar is less injury prone than the median first choice PL CB when ordered by games missed surely means that the two conclusions we can draw are that either he isn't injury prone or that he is but the term 'injury prone' has such a weak definition that more CBs than not qualify and therefore the concept is irrelevant.
*This list was hastily compiled and is probably incomplete.