I don't really see any harm in the rule, and it bodes well for both teams to have this option. I truly believe people underestimate the fatigue modern time players go through with the sheer amount of minutes they spend on the field, especially when you consider that ET mostly comes into play in a later stages of the season (in CL & EL) where it is more of a concern on the players, of course there are exceptions with some domestic cups. Playing those added minutes could easily injure players.
Ronin makes a great point, that shit should be changed ASAP. It's ridiculous how it strongly favours a team on the other in an unfair way.