I'm serious: the punishment must match that of Clyde. For their result simply to stand is no punishment as they lost the match. This will be very interesting indeed.
I haven't read the SFA rules, but I would be surprised if there is any points deduction in this case. The aim will not be to deduct points simply for the fact of having fielded an ineligible player, but whether that player had influenced the particular match in which they played.
If the offending team won the match (as Clyde did with us), then they did so unfairly (under the rules) and the match was therefore treated as a Rovers win. Had QP won or drawn their match, they would have had those points deducted and Cowdenbeath awarded 3. As it is, QP lost the match and therefore did not profit from breaking the rules, and Cowdenbeath did not lose out either. Therefore QP will probably get a fine and a slap on the wrists and the 3-0 result allowed to stand.