My Squadron mates and I have been discussing the same thing. We believe that there should be some protection against AFK'ers, particularly in PvP, and that it should be fairly simple to implement. If the system detects you are not moving, healing, or doing damage for a period longer than 60 seconds at the beginning of a match, and then perhaps for a 90-120 second period later in the match, it boots you. I might even go with a shorter period, perhaps as short as 30 seconds, at the beginning simply because perhaps it could substitute another player for the afk'er. There has to be some leeway for folks with lag or bad connections, especially when those problems originate from Cryptic's end, but still...there's no excuse for hitting "engage" and then walking away at that particular point for several minutes unless you are in a private match.
I am generally against micromanaging of players by the GM's and devs, and am generally against leaver's penalties or at least against any increase of them, but AFK penalties I am in support of after witnessing the rise in AFK'ers in PvP on the Federation side. It seems more rare in STF's, although I got trolled badly by a pair of intentional AFK'ers who sat out of an entire ISE while heaping abuse on the other three players.
P.S. One thing I do these days if I have the time is to report AFK players to their own fleetmates via PM's. If they are from a fleet full of bad eggs they won't care, but I'd say most fleets do care when their reputation is threatened.
Former/Cryptic Name: Captain_Hans_Langsdorff
Founding member, Special Service Squadron
"Fear God and Dread Nought." First Sea Lord, Adm. Jacky Fisher