I like the idea, however I had my own server and know a lot about the commands which can apply. As someone mentioned blocking the command really only blocks the command, so when someone flies into the PVP area they can still fly. There is another problem, if it would be possible to deny fly in the PVP you would fall down and die when you fly over it (cruising at high altitude .... BAM !!! you die). So I really think this is not possible, the only possibility would be to relocate the PVP arena to a PVP world, which would give the server more stress, thus more lag and so on.... As someone else mentioned, try PVP in the mineworld.

 

I found this plugin a while back, haven't tested it yet but it sounds like it would do the job.
http://dev.bukkit.org/server-mods/worldguard-fly-flag/

 

i so agree i posted a thread of the same thing

 

+1 if you really want to fly for pvp, then you can pay for fly+ to pvp in mining world. The pvp arena is open to all worst of ranks from builder to ecoleader! It seems unfair for a new player on ECC to see people flying around the arena. Either that, or make a fly enabled, and a fly disabled arena. Flying while in pvp is a HUGE game changer and you can rarely kill people with fly. Also, people with fly can use their speed to give a HUGE knock back to the back of the arena so you can not escape. This discourages much pvp, as I currently do not pvp as much because of fly

 

Well Most people Purchase FLy To Use it in pvp so...

 

It would be unfair to make it illegal to fly in the pvp arena. Some people bought fly just to pvp and taking it away would be like taking away fly from them. If this were to happen, everyone should be able to get a refund for fly if they want to.