The problem with the Rooney Rule now causing its ineffectiveness is the timing aspect. Teams zero in on a target coach and want that coach. If that coach is a white guy, then they find the first black guy they can find to check the Rooney Rule box so that they are allowed to hire their actual target before someone else does - see the Thomas Brown and David Shaw interviews above. Everyone knows those guys are not getting hired, so that is a complete circumvention of the intent of the rule, a giant waste of time, and gives the rule the perception of being a complete joke.
If there was a separate rule, which there should be for plenty of reasons not the least of which is to prevent teams from interviewing coaches who are actively preparing for playoff games, that said no team can hire a new head coach for the subsequent season between say December 1 and March 1, then it would take away the time crunch and teams would have the ability to conduct meaningful interviews. If a team has to wait 3 months before hiring someone anyway, then it eliminates the need to find the first black guy they can to check the box. Even if they have initially zeroed in on Harbaugh, if they can't hire him for a few months then there is no harm in taking plenty of time to interview other legitimate candidates.