I would tend to agree, in a perfect world at least. In the past I didn't think that Cryptic could ever pull it off, that they should cut their losses and go with something more GW-like, but now I'm not entirely sure
That said, some items (not gear) should be turned off. The fleet bonuses for example rightfully don't have an effect in PvP. The same should be true for bonuses you get from doff missions, consumables like ablative jevonite, and of course team batteries, but sadly isn't. I wouldn't mind seeing deuterium disabled in PvP either, I certainly wouldn't miss grinding it.
There's a simpler way that doesn't knock achievement as hard:
Instead of disabling those buffs, have an alternate way for PvPers to get all of them.
My BIG idea here is a method of paid PvP tournaments, which I think is necessary to support PvP development under F2P.
Here's the deal:
Cryptic releases a variety of ships BALANCED AGAINST ONE ANOTHER. Not perfectly balanced against anything else. Just eachother.
These ships cost a premium amount, more than normal ships.
For 3 months or 6 months, Cryptic has a PvP tournament. Which can only be queued for using these ships. Rewards might include things like Fleet-tier upgrades of the PvP ships, a special hull texture for all your ships, etc.
At the end of the tournament, the ships go down in price to 2500 or 2000 ZEN. This is more or less stated upfront than the higher cost is your "Tournament Entry Fee."