I wish I could tell you, just how very many BW lunch meetings, the topic of "Well WoW did ~this~ so we should too." came up in.
The ugly truth is, this game was designed from the ground up to be a cash cow for EA much like WoW is for Acti-Bliz.
It's apparent that they are similar games, with the considerable difference of Customer Service Support *which is inexplicably terrible in SW:TOR*.
With that said, I agree fully that PVP should be left right out on a PVE server. Other than Warzones, and the like. In my opinion, in no game, should a PVE server EVER have an auto-flagging zone. Period. I appreciate that waters down the "We're in the middle of a war." atmosphere in the game, but I'm not paying $15 a month to feel like I'm in a war. I'm paying, and playing, to relax at the end of a stressful day at work, or because I simply need a break. I'm doing so because I want to play a game where I can mindlessly do my own thing for a few hours without having to worry about the wife, or kids, or pets, or anything else in the world.
PVP'ers aren't bad people, I'm not saying that at all. Even I enjoy some periodically. However, balancing the PVP/PVE aspect in WoW brought about Reslience. A stat that was great for the PVP'ers but to everyone else was a message of "Congrats, now you'll never win another gank or be a realistic opponent in a Battleground." It was this stat that drove me to eventually cancelling my account. I don't have the time to spend grinding said gear, nor the inclination. However, if something isn't done, SWTOR will more than likely end up taking the same path.
I hope certain developers will see my post, and think about what I'm saying. Perhaps discuss this issue instead of what WoW did at the next meeting.