Hey Railz,
Frankly, I'm kinda with you. I don't take much joy in killing alliance even though with 4 teams of 5 level 80 toons I can steamroll them any time I want. So if you take out the "fun" of randomly ganking alliance, you are left with the inconvenience of alliance screwing with you. This really wasn't bad with RAF on Mag - I rerolled Mag in September and had nothing but level 1s. I leveled my first team normally (questing in different zones all the way to 80), but my other teams I leveled exclusively in the Ghostlands, SM, and Stratholme (where no allies can mess with ya) with a level 80 boosting them. Didn't have much of a problem with allies when leveling my teams past the RAF levels (60-80) either. Sure, occasionally you'll find an Asshat who wants to camp you, but with as many teams as I was leveling if that happened I'd just log off my current team and hop on another one.
I have a ton of 70s on an alliance PvP server (Stormreaver) from server open 3+ years ago and I remember ganking was MUCH worse then. For some reason on Mag it hasn't bothered me much - a combination of a shift in attitude (getting on a new team early and treating it as a minor inconvenience if it happens), leveling largely in instances, and what I perceive is less ganking in general than on Stormreaver.
And I guess it does add a bit of extra flavor when you meet a number of allies that kind of face off in front of you and you don't know if they are going to /dance and /wave or start attacking. Knowing if they are jerks I can quickly run back and wipe them with five toons makes me feel a lot better about things. One morning it was especially satisfying. I actually 10-box now and have found I can cut daily running time if I run 2 teams roughly in parrallel. One asshat attacked and killed one of my teams while they were on the harpoon shooting quest (in which you are largely defenseless). He wiped that team and was doing /sit on me repeatedly when I flew up 10 seconds later with another team of 5 and 2-shotted him. Though I get no pleasure whatsoever from ganking indiscriminantly, I *do* get some pleasure from killing asshats. And with two teams on at once I can do a very nice job of camping :)