More tokens for pvp would mean more AFKers in pvp.
Maybe, but I can't see a lot of people actually doing this for 1 emblem every 3 matches. If you really want to grind emblems at that sort of pace, it would be a lot more productive to get them by farming anomalies and completing just the quick (non-killing) explore missions. And that's assuming you have done all of the Deferi, Eta Eridani, and Fleet Action dailies for the day, which does not take a trivial amount of time.
If /afk'ing is a problem, then the solution is making it so you can't complete a match while /afk. Just slap a ten or twenty second /afk kick timer on these instances and most people would die of boredom before they could manage to complete even one match.