This isn't a "say nothing." Throw your opinion out there, nobody wants to stop you. (Well, I don't.)
However, (a) you are, from your post, basing this on poor information (that it's somehow related to PVP - it isn't, that's a side effect of the command being there when it shouldn't, and there are other exploits related to it,) and (b) yes, it does come off as "change this and I'm leaving." Even if it's just "backing off," well - personally, it comes off as a (poor, and that's not "because it's from you," I'm not aiming this at you personally, just the type of post) threat to a team that's running this and developing it on a *volunteer* basis. Which, yes, a "me" thing but does tend to put my back up and get that reaction.
And, (c) as mentioned - you're doing this without seeing if they have something else they're replacing it *with.* The devs aren't blind that people like the functionality. Give them a little credit and see what they're *doing* before complaining about them doing what they've said they'll do for... what, over a year now?
Honestly, in general I'm somewhat baffled by this. Base *passcodes* aren't going away. All those transport hub bases will still be useful. The base teleporter option (which, yes, has a recharge, but how often do you need to run down to the base?) takes base passcodes. There are multiple other fast-transport options, both as purchased/earned and (granted, requiring other picks, unless you're a 'shade) pool powers. It's not like this one command goes away and you're forced to [Walk] from N to S Independence Port for everything you want to do. And those powers will likely be involved in some way with this change.
Wait and see. Get involved in the betas if you really want to give feedback and shape this - this doesn't mean "spend 40 hours a week," but even half an hour when they announce something's there to take a look at can shape what's done.