I think it would be a good idea to subtract merits and Honor points for both feds and Klings that leave PVP matches leaving teams horribly unbalanced or a team of 5 people stuck on a map with nothing to do, that or add a Timer to matches that ends it after X amount of time.
Popped in late to a Cracked planet pug, cloaked and started making my way across and went huh when I reached my side of the middle of the planet. A line of Fed ships, single filing it through the middle of the planet lead by an escort, 3 sci ships and a cruiser. Odd I says, so did a 180, come out of the middle to watch what happens and see if maybe the Feds are going to set up a spawn camp and position myself to at least hit the escort if they do. They were not, but I did notice 4 klingons coming over the top of the planet heading from the Fed spawn gate. Accepted the team invite and asked WTF was with the Feds. Was told that they had just got to the Fed side and watched the Feds spawn, when the escort and cruiser driver started going on in zone about how the klingons were 'still' cloaked and then they went shooting off to our spawn gate followed by the sci ships. The escort and cruiser had warped out by now. It was like we all looked at each other, shrugged, de-cloaked and popped those 3 sci ships. The fed side in that match never really recovered after that. Time from when the Feds were observed to have spawned and the escort et al warped... ~2-3 minutes. That escort and cruiser driver lost that match for the sci ships.
FvF with no cloak is your solution, not a timer. As to penalizing, the escort and cruiser did not earn anything, but those sci ships sure got shafted with the looser rewards.